viralrecon gets stuck on FASTQC jobs

I try to run viralrecon for 86 samples. It seems the pipeline gets stuck and I cannot figure out why. I did run the pipeline on my local machine (14 cores, 128 GB memory) with standard configuration like this:
nextflow run nf-core/viralrecon --input /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//samples.csv --protocol amplicon --amplicon_bed /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.bed --amplicon_fasta /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.fa --genome MN908947.3 --skip_assembly --outdir /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//results -profile singularity -with-singularity /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//singularity.dev.961b10463ae1.sif -r e49cee2

it starts to run, but then it gets stuck without an error and just seems to hang. There is no CPU usage according to htop. When I run the pipeline on our cluster, distributing jobs with SGE, I get a similar issue. First, I thought it is SGE, but now that the pipeline also gets stuck on my local machine. Getting stuck means, there is no new entry in the log for 1.5 hours now. From the log, I can see that the last jobs were FASTQC jobs. What can I do, do you need more infos? I attach the log.
`.nextflow.log`

Jan-29 16:04:40.079 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon --input /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//samples.csv --protocol amplicon --amplicon_bed /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.bed --amplicon_fasta /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.fa --genome MN908947.3 --skip_assembly --outdir /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//results -profile singularity -with-singularity /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//singularity.dev.961b10463ae1.sif -r e49cee2
Jan-29 16:04:40.130 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.10.0
Jan-29 16:04:40.824 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 16:04:40.835 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 16:04:41.024 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/viralrecon` [condescending_volhard] - revision: e49cee2f15dce2e9993736d16f08b1f9d808e292
Jan-29 16:04:41.596 [main] DEBUG nextflow.scm.AssetManager - WARN: Cannot find any Git revision matching: null; ls-remote: [Ref[refs/pull/104/head=e21a9d69c8a80c902e8ed67ead97269ae040daa8], Ref[refs/pull/71/head=de556ff67b80ef002b437391fe3e8ae86ddfcca7], Ref[refs/pull/85/head=cea8613b4a939db7dc36fb639b0b05de07a9aaed], Ref[refs/tags/1.0.0=7422b0d353b1a295fb7cda47f2f7750c3bd890d1], Ref[refs/pull/69/head=b6e20251447dff08ea213605f4bfe554b17a0ab4], Ref[refs/pull/40/head=658104370a3aab1bde5e176750a1ae15687a0b89], Ref[refs/pull/24/head=b77d015ce4720e7447ee6c50fcca8758d16a173e], Ref[refs/pull/135/head=778693daee7a476c8cc9ed1b703bd0e801d42016], Ref[refs/pull/55/head=3bfc2ba5239baa54260a95f031523f4e212451f6], Ref[refs/heads/dsl2=c8f708819bede4b1c8f3840c6355c22b03e6d0e9], Ref[refs/pull/23/head=a87af4acb8a3afe26175da6feeb4c5ca28b3b436], Ref[refs/pull/148/head=9ba237e45aef44056dfd137caf33782252b8c9b2], Ref[refs/pull/120/head=4461c408701db0ba78264092632e45c93f83ba4c], Ref[refs/pull/103/head=372de46851a76d35c038fdf4a80d1207f71de073], Ref[refs/pull/68/head=487df0392fa1579abb9842d33111ebcc6e223d66], Ref[refs/pull/70/head=fb6596249daf33376ca148c6b06a9f2ebb50af8d], Ref[refs/pull/118/head=fb552abe4143334b8b6131028e029a6d9271202a], Ref[refs/pull/150/head=74e32eeb8efa98fea152899ae9e5f43f0aefe087], Ref[refs/pull/38/head=6030094912cb345c1b16584a713c0b94595003e0], Ref[refs/pull/134/head=abcd646b49cd7bccc8e8c4ddf164782731e1eb56], Ref[refs/pull/54/head=4c4103b9fda02bf60c8f77e424ab11d0b783e43e], Ref[refs/pull/99/head=6756a4e3a518e2cac416550168a6b89c57975785], Ref[refs/pull/98/head=afc1fd67c633482675226db3906f9e0ed93ab56f], Ref[refs/pull/84/head=52db59ea24b462f0760896bdeb2f743c85a8b781], Ref[refs/pull/11/head=886c2f681f33e75858deb6e9d1c914fdb299c035], Ref[refs/pull/39/head=0b12a3e4f87ca8f0f83fbde0737466268e15785c], Ref[refs/pull/87/head=d3c56f47a3a51a50a526590901e3f1bfe3db6049], Ref[refs/pull/116/head=e1134ed88cec082d6f7373ba96bfc4e0ecc412bc], Ref[refs/pull/119/head=43c9d78884774bfe5e419014c38cf1e8b31c6710], Ref[refs/pull/41/head=4853f86c0869171b16a53b767401a5a341167e53], Ref[refs/pull/36/head=3eaeb42a7b15701ec7107498e5cdd5866325143c], Ref[refs/pull/52/head=9e511349d7e899310a41fa9b46269571e39034f5], Ref[refs/pull/22/head=a580cfaa886907f4cda826088a15cc8241a99c31], Ref[refs/pull/102/head=1b93695f72a814764cc7dbf74d6a47855042b87a], Ref[refs/pull/25/head=6ebfb8a9d9c42dc06827211f6ef576bdee232efa], Ref[refs/pull/105/head=9a46ba7d317c00e23bdfb889dd1298c33171c99c], Ref[refs/pull/146/head=90079b0fa5d37ffd551c4a9a18cba4f9860a017b], Ref[refs/pull/49/head=fee3c68ef7053fc9bd79a11937320abd056f0948], Ref[refs/pull/88/head=00816d0ec217c4adc2fa38ea07ef882d4dd1c822], Ref[refs/tags/1.1.0=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/140/head=2898d227ba61e2920fc4cc36ed6e5cd14064b7f7], Ref[refs/pull/60/head=eaab9880c914ea28d55f9077005808b9034a60ab], Ref[refs/pull/18/head=23ef7e0cacaa1726777c2a00dd7d138948f99fe8], Ref[refs/pull/82/head=7f8c7988f95c339debce2b3570df0f399fc230e0], Ref[refs/pull/21/head=4a485b793c961d148fae1bbf7f202b49a28307a3], Ref[refs/pull/65/head=3d6512ac4e109958c5fbf719ccbbd14ed9004017], Ref[refs/pull/27/head=775379f647f9e2e41a0dee869dd31d9fef06a9df], Ref[refs/pull/145/head=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/pull/43/head=2e5a2b4772239651bd292cbdd1d21fc69c4d1caa], Ref[refs/pull/129/head=7b38fe2439f97927093452232263123e71368d44], Ref[refs/pull/59/head=046d91a78b5c112a93ed7ef7d185c18a19bea8b9], Ref[refs/pull/139/head=60cd93051c5de0af9f79886e48d7c96c6b4ae199], Ref[refs/pull/53/head=ac36d1fcf11674ab8ccf8b77a7bfb414614b9cad], Ref[refs/pull/111/head=69326f97b1c1d1b8733a0df573cb1f3eff907e6d], Ref[refs/pull/136/head=7002a5eb6f481075cf577e7898212bf01144e2f9], Ref[refs/pull/130/head=b0229bbbc6eda0614aa40269a3f06b4edf78c360], Ref[refs/pull/117/head=acfc523f35cb9174c383b01cede82a14c8818688], Ref[refs/pull/133/head=52a1e50ff57cf2295e2de9b425f73f276f20bade], Ref[refs/pull/37/head=55c2a56f7101f4d9bc74fa91cbc6bf9fd81527e2], Ref[refs/pull/114/head=d0e3e179d14b95eb8a1b08c3edcea5012e741206], Ref[refs/pull/34/head=dad04235f8b75dabd385a2e2476a895629549d98], Ref[refs/pull/50/head=fc6eb38364aa85181defa21fb32ba9c56b87bd80], Ref[refs/pull/72/head=3c810f848c21ca58d69aa31b0cecb68889cecebd], Ref[refs/pull/97/head=c6682e57fd58b9ed743e388999c393f2cdaccd78], Ref[refs/pull/78/head=7c38d49a99fd897ac473995c29876c5579e1722d], Ref[refs/pull/91/head=b0f9b52f9d17ba097a518b4dd01e25da52c6159a], Ref[refs/pull/75/head=f9b4b596671b2325011c42734b14239027d62c1d], Ref[refs/pull/94/head=f7004dd083f523674b0b5b7b3d98176b8887b43e], Ref[refs/pull/32/head=cb10b45cadedd90d5da6460704d5cd5f15764c01], Ref[refs/pull/77/head=ed2511444ce83e7924e9fd91584c268251bb2e31], Ref[refs/pull/63/head=4f56a2b91f580fc4f1ff4ff9510bd675b1d512b0], Ref[refs/pull/29/head=634bf562df7712e80ffa57839263273a53b3ae6b], Ref[refs/pull/16/head=79005a50623da53a812584537ee081744631dbe2], Ref[refs/pull/93/head=a495c1c40bd21085c21247ad812e51bcbb90088f], Ref[refs/pull/76/head=8b7285dbb0baa5ee300a43500dbeff782b284134], Ref[refs/pull/15/head=f899da38519e283a12df70fa6f20efd0a851f053], Ref[refs/pull/126/head=13331866195d9b0cc0aee95fc0df881965be7ef3], Ref[refs/pull/62/head=edb5bd0b6f40ac15432d5d234293d39334fd347f], Ref[refs/pull/92/head=ecc1fdcf1dade61baa2f65c2904f88457aa54054], Ref[refs/pull/28/head=c83b9a771430ed9c793e78f4507b6ba50858950b], Ref[refs/pull/81/head=9b4444fc1bb6ea038245dcb57db55ff96161d977], Ref[refs/pull/79/head=d9ad5b9c6f6ee7e1c2e62c36d8df2ef13eecffc1], Ref[refs/pull/44/head=a6524572ebfc9a9b73b1c207d7b56f3c0c37a411], Ref[refs/pull/110/head=9ea4c1a52a0b55beb8fda28d9d5d318c7909a99c], Ref[refs/pull/7/head=053508707e945f883dd611cb6eab89be73f77f56], Ref[refs/pull/127/head=0a7325e0a42b5f06afcb622c74962a3899157eca], Ref[refs/pull/108/head=2622959ec0ca9753ccf35fb57fa38d12a688a4f2], Ref[refs/pull/30/head=8940416aacf0648eeef5fd083cc7cc333d266be4], Ref[refs/pull/17/head=747296441fb64b4bd1137fd8d93f08f91572f90b], Ref[refs/pull/74/head=72d240b1e367193672c4e8914ffd7d51c93fa39b], Ref[HEAD=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/35/head=3781ff8ee824eb0c63644145a48e45221e22de9a], Ref[refs/pull/132/head=5b355cd205b4fa66a6658500d3080481d02bc736], Ref[refs/pull/90/head=b2eef6ca9038df66be27c985372ca1125fc3d8a7], Ref[refs/pull/58/head=5d42f5891d40e249a27a5cc1dcff8e9c13ce78af], Ref[refs/pull/131/head=30db7f95649e6e4f309067f3acb15b86c4499c6d], Ref[refs/pull/20/head=5c7bd7013a253a9785b346f65cf9bfc898da48f6], Ref[refs/pull/137/head=ee5b7b7a47ddabc6b44ef203ce13599ed3e42079], Ref[refs/pull/51/head=6cc01895b3db2901ac33dad5ae2317664467ae35], Ref[refs/pull/19/head=29d89516b218140ce2a5ed4f04c7898d436fc390], Ref[refs/pull/100/head=85f13dd3df92feec87fbe5b367715bb53743067c], Ref[refs/pull/73/head=d07af1ccde076f7010330c1fdd7d60a7b4c6f5be], Ref[refs/pull/96/head=2d5cdb3d8234e7f11c079fe57d8b131010423aae], Ref[refs/pull/57/head=d72c512df8fd38215b8c9bc259a2b97373536ad0], Ref[refs/pull/125/head=c9d40fb3c3f0bf413d593d43c6483f0eca234249], Ref[refs/pull/128/head=eca1bdcdaed5aefaf74402c858a45dc1ba4d123a], Ref[refs/pull/64/head=f27a55065c359cc6f19c4ea8bd7b6d93375a8141], Ref[refs/pull/48/head=e0474ce0f9f7c198f5e49070536b76c70e4b2e0b], Ref[refs/pull/45/head=0687ec1ef98f3ae80c147329c193338d79f537d6], Ref[refs/pull/106/head=160438169ebb0e488fd75f4706dc6fb66888cd7f], Ref[refs/pull/109/head=a5c12fcbbe4ead170ccd13d54b2038406757f271], Ref[refs/heads/TEMPLATE=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/heads/dev=e49cee2f15dce2e9993736d16f08b1f9d808e292], Ref[refs/pull/83/head=d9589698b6189d60f996fc722d566f84c28215c2], Ref[refs/pull/86/head=5ac0f286bc4acf243ba7ea53a665fe24ab02f85b], Ref[refs/pull/141/head=052e9a8cdaa1260a6007571b97acc855b7513086], Ref[refs/pull/131/merge=103c74d77174b79e1060b5757209a016c1e26aa6], Ref[refs/heads/master=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/80/head=80a8eb55a94c26d7c488cf0290ff3dc904c3c42d], Ref[refs/pull/89/head=397f25529d0ca506666c88d74a5382fcbbbb481e], Ref[refs/pull/144/head=b006a4187540d86a80981d28c364779ffb2c4aeb], Ref[refs/pull/147/head=80b17e725ec72e03ee63be69187b0f2feb7e8ada]]
Jan-29 16:04:41.629 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 16:04:41.630 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 16:04:41.640 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jan-29 16:04:42.104 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, test_sispa, denbi_qbic, bi, genotoul, bigpurple, uppmax, abims, imperial_mb, docker, gis, utd_ganymede, mpcdf, conda, test_full_sispa, singularity, icr_davros, munin, prince, podman, test_sra, czbiohub_aws, hebbe, cfc, uzh, ccga_med, debug, test, genouest, cbe, ebc, ccga_dx, crick, google, kraken, phoenix, seg_globe, shh, awsbatch, pasteur, uct_hpc, imperial, test_full, binac]
Jan-29 16:04:42.116 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null`
Jan-29 16:04:42.154 [main] DEBUG nextflow.Session - Session uuid: d50953bf-81a8-400d-bca1-9b94a03c8b75
Jan-29 16:04:42.154 [main] DEBUG nextflow.Session - Run name: condescending_volhard
Jan-29 16:04:42.155 [main] DEBUG nextflow.Session - Executor pool size: 28
Jan-29 16:04:42.172 [main] DEBUG nextflow.cli.CmdRun -
  Version: 20.10.0 build 5430
  Created: 01-11-2020 15:14 UTC (16:14 CEST)
  System: Linux 5.4.0-58-generic
  Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 11.0.8-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 3558564@cbioinfws1 [<IP_ADDRESS>]
  CPUs: 28 - Mem: 125.5 GB (47.1 GB) - Swap: 14 GB (13.9 GB)
Jan-29 16:04:42.187 [main] DEBUG nextflow.Session - Work-dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work [zfs]
Jan-29 16:04:42.230 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jan-29 16:04:42.234 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-29 16:04:42.408 [main] DEBUG nextflow.Session - Session start invoked
Jan-29 16:04:42.411 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/results/pipeline_info/execution_trace.txt
Jan-29 16:04:45.536 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-29 16:04:45.543 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: MOSDEPTH_GENOME, UNICYCLER_PLASMIDID, UNICYCLER_SNPEFF, MINIA_BLAST, output_documentation, UNICYCLER_VG, IVAR_CONSENSUS, SORT_BAM, FASTP, SRA_FASTQ_FTP, UNICYCLER_ABACAS, PICARD_MARKDUPLICATES, MINIA, VARSCAN2, BCFTOOLS_CONSENSUS, CAT_FASTQ, METASPADES_SNPEFF, GUNZIP_GFF, SPADES_VG, UNICYCLER_QUAST, PICARD_METRICS, KRAKEN2, SPADES_PLASMIDID, METASPADES_QUAST, BCFTOOLS_VARIANTS, BCFTOOLS_SNPEFF, MAKE_BLAST_DB, MOSDEPTH_AMPLICON, METASPADES, IVAR_VARIANTS, FASTQC, BOWTIE2_INDEX, SPADES, METASPADES_VG, SPADES_ABACAS, METASPADES_PLASMIDID, SPADES_SNPEFF, UNICYCLER, MULTIQC, CUTADAPT, KRAKEN2_BUILD, IVAR_TRIM, IVAR_QUAST, UNICYCLER_BLAST, VARSCAN2_QUAST, METASPADES_ABACAS, MINIA_VG, MINIA_ABACAS, get_software_versions, SPADES_BLAST, MINIA_SNPEFF, SPADES_QUAST, MAKE_SNPEFF_DB, BCFTOOLS_QUAST, SAMTOOLS_MPILEUP, GUNZIP_FASTA, METASPADES_BLAST, BCFTOOLS_ISEC, VARSCAN2_SNPEFF, MINIA_QUAST, UNTAR_KRAKEN2_DB, MOSDEPTH_AMPLICON_PLOT, SRA_FASTQ_DUMP, MINIA_PLASMIDID, BOWTIE2, IVAR_SNPEFF, CHECK_SAMPLESHEET, VARSCAN2_CONSENSUS
Jan-29 16:04:45.772 [main] INFO  nextflow.Nextflow - ----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/viralrecon v1.2.0dev
----------------------------------------------------

Jan-29 16:04:45.775 [main] INFO  nextflow.Nextflow - Run Name              : condescending_volhard
Samplesheet           : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//samples.csv
Protocol              : amplicon
Amplicon Fasta File   : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.fa
Amplicon BED File     : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.bed
Amplicon Left Suffix  : _LEFT
Amplicon Right Suffix : _RIGHT
Viral Genome          : MN908947.3
Viral Fasta File      : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz
Viral GFF             : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz
Fastp Mean Qual       : 30
Fastp Qual Phred      : 30
Fastp Unqual % Limit  : 10
Fastp Min Trim Length : 50
Variant Calling Tools : varscan2,ivar,bcftools
Min Mapped Reads      : 1000
iVar Trim Min Len     : 20
iVar Trim Min Qual    : 20
iVar Trim Window      : 4
Mpileup Depth         : 0
Min Base Quality      : 20
Min Read Depth        : 10
Min Allele Freq       : 0.25
Max Allele Freq       : 0.75
Varscan2 Strand Filter: Yes
Skip Kraken2          : Yes
Skip Assembly         : Yes
Max Resources         : 128.GB memory, 16 cpus, 240.h time per job
Container             : singularity - /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//singularity.dev.961b10463ae1.sif
Output dir            : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//results
Publish dir mode      : copy
Launch dir            : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore
Working dir           : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work
Script dir            : /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon
User                  : fabirost
Config Profile        : singularity
Jan-29 16:04:45.775 [main] INFO  nextflow.Nextflow - ----------------------------------------------------
Jan-29 16:04:45.814 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name GUNZIP_FASTA
Jan-29 16:04:45.816 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:45.816 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:45.820 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-29 16:04:45.824 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=28; memory=125.5 GB; capacity=28; pollInterval=100ms; dumpInterval=5m
Jan-29 16:04:46.130 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name GUNZIP_GFF
Jan-29 16:04:46.132 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.132 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.137 [Actor Thread 3] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=84; maxQueueSize=252; keepAlive=1m
Jan-29 16:04:46.148 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.148 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.148 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz to work dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/stage/d4/6f01f2da9b3e9df329929a24dab4e4/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz
Jan-29 16:04:46.216 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SRA_FASTQ_FTP
Jan-29 16:04:46.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name SRA_FASTQ_FTP
Jan-29 16:04:46.217 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SRA_FASTQ_DUMP
Jan-29 16:04:46.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name SRA_FASTQ_DUMP
Jan-29 16:04:46.228 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.228 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.249 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FASTQC
Jan-29 16:04:46.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.255 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FASTP
Jan-29 16:04:46.255 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.255 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.261 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BOWTIE2_INDEX
Jan-29 16:04:46.261 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.261 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.265 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name MAKE_SNPEFF_DB
Jan-29 16:04:46.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BOWTIE2
Jan-29 16:04:46.277 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.277 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.283 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SORT_BAM
Jan-29 16:04:46.284 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.284 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_TRIM
Jan-29 16:04:46.292 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz to work dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/stage/65/d4783068a1abebd25f22a3dc83edcd/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz
Jan-29 16:04:46.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.297 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PICARD_MARKDUPLICATES
Jan-29 16:04:46.298 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.298 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PICARD_METRICS
Jan-29 16:04:46.303 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.303 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.307 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_GENOME
Jan-29 16:04:46.308 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.308 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.310 [Task submitter] INFO  nextflow.Session - [02/05e8a9] Submitted process > CHECK_SAMPLESHEET (samples.csv)
Jan-29 16:04:46.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_AMPLICON
Jan-29 16:04:46.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.314 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.321 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_AMPLICON_PLOT
Jan-29 16:04:46.321 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.321 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SAMTOOLS_MPILEUP
Jan-29 16:04:46.325 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.325 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.329 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2
Jan-29 16:04:46.330 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.330 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.336 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.336 [Task submitter] INFO  nextflow.Session - [0e/cd6472] Submitted process > GUNZIP_FASTA
Jan-29 16:04:46.339 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_CONSENSUS
Jan-29 16:04:46.340 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.340 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.346 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_SNPEFF
Jan-29 16:04:46.346 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.346 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.351 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_QUAST
Jan-29 16:04:46.351 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_VARIANTS
Jan-29 16:04:46.358 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.358 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.364 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_CONSENSUS
Jan-29 16:04:46.364 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.364 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.368 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_SNPEFF
Jan-29 16:04:46.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_QUAST
Jan-29 16:04:46.373 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.373 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_VARIANTS
Jan-29 16:04:46.376 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.376 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.381 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_CONSENSUS
Jan-29 16:04:46.381 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.381 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.384 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_SNPEFF
Jan-29 16:04:46.385 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.388 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_QUAST
Jan-29 16:04:46.388 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.388 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_ISEC
Jan-29 16:04:46.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name BCFTOOLS_ISEC
Jan-29 16:04:46.393 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.393 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.396 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MAKE_BLAST_DB
Jan-29 16:04:46.396 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.396 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.398 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.400 [Task submitter] INFO  nextflow.Session - [e1/00bc46] Submitted process > GUNZIP_GFF
Jan-29 16:04:46.401 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name SPADES
Jan-29 16:04:46.401 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES
Jan-29 16:04:46.402 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.402 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_BLAST
Jan-29 16:04:46.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_BLAST
Jan-29 16:04:46.406 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.406 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_ABACAS
Jan-29 16:04:46.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_ABACAS
Jan-29 16:04:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.413 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_PLASMIDID
Jan-29 16:04:46.413 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_PLASMIDID
Jan-29 16:04:46.413 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.413 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_QUAST
Jan-29 16:04:46.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_QUAST
Jan-29 16:04:46.418 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.418 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_VG
Jan-29 16:04:46.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_VG
Jan-29 16:04:46.423 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.423 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_SNPEFF
Jan-29 16:04:46.427 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_SNPEFF
Jan-29 16:04:46.427 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.427 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name METASPADES
Jan-29 16:04:46.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES
Jan-29 16:04:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_BLAST
Jan-29 16:04:46.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_BLAST
Jan-29 16:04:46.434 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.434 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_ABACAS
Jan-29 16:04:46.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_ABACAS
Jan-29 16:04:46.438 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.438 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.442 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_PLASMIDID
Jan-29 16:04:46.442 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_PLASMIDID
Jan-29 16:04:46.443 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.446 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_QUAST
Jan-29 16:04:46.446 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_QUAST
Jan-29 16:04:46.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_VG
Jan-29 16:04:46.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_VG
Jan-29 16:04:46.451 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.451 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.454 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_SNPEFF
Jan-29 16:04:46.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_SNPEFF
Jan-29 16:04:46.455 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.455 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name UNICYCLER
Jan-29 16:04:46.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER
Jan-29 16:04:46.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_BLAST
Jan-29 16:04:46.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_BLAST
Jan-29 16:04:46.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.467 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_ABACAS
Jan-29 16:04:46.468 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_ABACAS
Jan-29 16:04:46.468 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.468 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.472 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_PLASMIDID
Jan-29 16:04:46.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_PLASMIDID
Jan-29 16:04:46.473 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.473 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.476 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_QUAST
Jan-29 16:04:46.477 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_QUAST
Jan-29 16:04:46.477 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.477 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_VG
Jan-29 16:04:46.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_VG
Jan-29 16:04:46.481 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.481 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_SNPEFF
Jan-29 16:04:46.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_SNPEFF
Jan-29 16:04:46.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.485 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name MINIA
Jan-29 16:04:46.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA
Jan-29 16:04:46.489 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.489 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_BLAST
Jan-29 16:04:46.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_BLAST
Jan-29 16:04:46.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_ABACAS
Jan-29 16:04:46.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_ABACAS
Jan-29 16:04:46.496 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.496 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_PLASMIDID
Jan-29 16:04:46.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_PLASMIDID
Jan-29 16:04:46.500 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.500 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.503 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_QUAST
Jan-29 16:04:46.504 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_QUAST
Jan-29 16:04:46.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_VG
Jan-29 16:04:46.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_VG
Jan-29 16:04:46.508 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.508 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_SNPEFF
Jan-29 16:04:46.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_SNPEFF
Jan-29 16:04:46.511 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.511 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions
Jan-29 16:04:46.524 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.524 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.555 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.555 [Task submitter] INFO  nextflow.Session - [99/ab7350] Submitted process > get_software_versions
Jan-29 16:04:46.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MULTIQC
Jan-29 16:04:46.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.598 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.602 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-29 16:04:46.602 [main] DEBUG nextflow.Session - Session await
Jan-29 16:04:46.611 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.613 [Task submitter] INFO  nextflow.Session - [3f/dfd1ac] Submitted process > output_documentation
Jan-29 16:04:46.702 [Actor Thread 4] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.011 s; total time: 0.012 s
Jan-29 16:04:46.713 [Actor Thread 4] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/8318f1e9fe9f83c0c4c05c6503d98304.collect-file
Jan-29 16:04:46.719 [Actor Thread 4] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-14007747180325198031
Jan-29 16:04:46.776 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: GUNZIP_FASTA; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/0e/cd64726e576234d6afd243e60470a4]
Jan-29 16:04:46.813 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GUNZIP_GFF; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e1/00bc46cbdd23a0a62eeddc73ee8b94]
Jan-29 16:04:46.813 [Task submitter] INFO  nextflow.Session - [2b/435f49] Submitted process > BOWTIE2_INDEX (GCA_009858895.3_ASM985889v3_genomic.200409.fna)
Jan-29 16:04:46.829 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.829 [Task submitter] INFO  nextflow.Session - [22/49fc18] Submitted process > MAKE_SNPEFF_DB (GCA_009858895.3_ASM985889v3_genomic.200409.fa)
Jan-29 16:04:46.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: CHECK_SAMPLESHEET (samples.csv); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/02/05e8a99959b4753cc597633450f804]
Jan-29 16:04:46.856 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `CHECK_SAMPLESHEET (samples.csv)` is unable to find [UnixPath]: `/home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/02/05e8a99959b4753cc597633450f804/sra_run_info.tsv` (pattern: `sra_run_info.tsv`)
Jan-29 16:04:46.942 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process CHECK_SAMPLESHEET > Skipping output binding because one or more optional files are missing: fileoutparam<1>
Jan-29 16:04:47.261 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.261 [Task submitter] INFO  nextflow.Session - [9d/c9edcd] Submitted process > CAT_FASTQ (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:47.368 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.368 [Task submitter] INFO  nextflow.Session - [c9/38ae42] Submitted process > CAT_FASTQ (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:04:47.372 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.372 [Task submitter] INFO  nextflow.Session - [23/47d98a] Submitted process > CAT_FASTQ (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:04:47.377 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.378 [Task submitter] INFO  nextflow.Session - [b6/c5cc2e] Submitted process > CAT_FASTQ (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:04:47.382 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.383 [Task submitter] INFO  nextflow.Session - [10/4619d2] Submitted process > CAT_FASTQ (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:04:47.388 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.389 [Task submitter] INFO  nextflow.Session - [7b/ee6817] Submitted process > CAT_FASTQ (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:04:47.394 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.394 [Task submitter] INFO  nextflow.Session - [53/5de058] Submitted process > CAT_FASTQ (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:04:47.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: BOWTIE2_INDEX (GCA_009858895.3_ASM985889v3_genomic.200409.fna); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/2b/435f49b16c5b5dcc5d9a8ca1dfd157]
Jan-29 16:04:47.488 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.489 [Task submitter] INFO  nextflow.Session - [dd/794e12] Submitted process > CAT_FASTQ (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:04:47.495 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.495 [Task submitter] INFO  nextflow.Session - [d2/0ab361] Submitted process > CAT_FASTQ (L66091_EdenPool_Covid-DD-VIR-00229)
Jan-29 16:04:47.498 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.499 [Task submitter] INFO  nextflow.Session - [5b/808949] Submitted process > CAT_FASTQ (L66082_EdenPool_Covid-DD-VIR-00211)
Jan-29 16:04:47.503 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.505 [Task submitter] INFO  nextflow.Session - [0f/a9d31b] Submitted process > CAT_FASTQ (L66100_EdenPool_Covid-DD-VIR-00244)
Jan-29 16:04:47.509 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.509 [Task submitter] INFO  nextflow.Session - [91/da743d] Submitted process > CAT_FASTQ (L66095_EdenPool_Covid-DD-VIR-00237)
Jan-29 16:04:47.513 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.513 [Task submitter] INFO  nextflow.Session - [81/4f7d3a] Submitted process > CAT_FASTQ (L66078_EdenPool_Covid-DD-VIR-00207)
Jan-29 16:04:47.578 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/dfd1ac62f7ef2fb814e8b064d80f69]
Jan-29 16:04:47.582 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.583 [Task submitter] INFO  nextflow.Session - [fc/9de7d1] Submitted process > CAT_FASTQ (L66088_EdenPool_Covid-DD-VIR-00221)
Jan-29 16:04:47.628 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: CAT_FASTQ (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9d/c9edcdd2549682ed2c4b8e90962be0]
Jan-29 16:04:47.633 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.633 [Task submitter] INFO  nextflow.Session - [35/b68bc5] Submitted process > CAT_FASTQ (L66090_EdenPool_Covid-DD-VIR-00226)
Jan-29 16:04:48.048 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: CAT_FASTQ (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/23/47d98a6a017a12cec1f39351ec4f4e]
Jan-29 16:04:48.052 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.052 [Task submitter] INFO  nextflow.Session - [21/f7ef2c] Submitted process > CAT_FASTQ (L66094_EdenPool_Covid-DD-VIR-00236)
Jan-29 16:04:48.089 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: CAT_FASTQ (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/7b/ee681796965d59b6601a420e6b9705]
Jan-29 16:04:48.093 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.101 [Task submitter] INFO  nextflow.Session - [8c/eb1e12] Submitted process > CAT_FASTQ (L66097_EdenPool_Covid-DD-VIR-00240)
Jan-29 16:04:48.169 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: CAT_FASTQ (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/38ae42802f24319657933d43c11a88]
Jan-29 16:04:48.172 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.173 [Task submitter] INFO  nextflow.Session - [15/592959] Submitted process > CAT_FASTQ (L66077_EdenPool_Covid-DD-VIR-00206)
Jan-29 16:04:48.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: CAT_FASTQ (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b6/c5cc2eaa84bde00df51f2b9defdaaf]
Jan-29 16:04:48.180 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.180 [Task submitter] INFO  nextflow.Session - [96/91d0cf] Submitted process > CAT_FASTQ (L66076_EdenPool_Covid-DD-VIR-00205)
Jan-29 16:04:48.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: CAT_FASTQ (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/10/4619d25993a419d6bf78914274350b]
Jan-29 16:04:48.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: CAT_FASTQ (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/53/5de058b8baff74a31723f581bac17f]
Jan-29 16:04:48.217 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.218 [Task submitter] INFO  nextflow.Session - [9a/86c686] Submitted process > CAT_FASTQ (L66098_EdenPool_Covid-DD-VIR-00241)
Jan-29 16:04:48.227 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.227 [Task submitter] INFO  nextflow.Session - [9c/76507b] Submitted process > CAT_FASTQ (L66079_EdenPool_Covid-DD-VIR-00208)
Jan-29 16:04:48.329 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: CAT_FASTQ (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/dd/794e1280831b70961b7616298e8de4]
Jan-29 16:04:48.332 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.332 [Task submitter] INFO  nextflow.Session - [38/1fbe20] Submitted process > CAT_FASTQ (L66081_EdenPool_Covid-DD-VIR-00210)
Jan-29 16:04:48.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: CAT_FASTQ (L66091_EdenPool_Covid-DD-VIR-00229); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d2/0ab3613df6a009215572ea4b8bf876]
Jan-29 16:04:48.423 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.424 [Task submitter] INFO  nextflow.Session - [e5/7db6cd] Submitted process > CAT_FASTQ (L66092_EdenPool_Covid-DD-VIR-00231)
Jan-29 16:04:48.516 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: CAT_FASTQ (L66082_EdenPool_Covid-DD-VIR-00211); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/5b/80894983db70c8227739ee8f242635]
Jan-29 16:04:48.519 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.519 [Task submitter] INFO  nextflow.Session - [81/23ed74] Submitted process > CAT_FASTQ (L66074_EdenPool_Covid-DD-VIR-00201)
Jan-29 16:04:48.730 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: CAT_FASTQ (L66095_EdenPool_Covid-DD-VIR-00237); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/91/da743ddc120f3302595b241ec606a4]
Jan-29 16:04:48.732 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.732 [Task submitter] INFO  nextflow.Session - [a4/5d0aa3] Submitted process > CAT_FASTQ (L66101_EdenPool_Covid-DD-VIR-00245)
Jan-29 16:04:48.806 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: CAT_FASTQ (L66100_EdenPool_Covid-DD-VIR-00244); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/0f/a9d31b11a58ba6896acfcfbf2083d8]
Jan-29 16:04:48.811 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.811 [Task submitter] INFO  nextflow.Session - [b0/e41d54] Submitted process > CAT_FASTQ (L66087_EdenPool_Covid-DD-VIR-00219)
Jan-29 16:04:48.814 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: CAT_FASTQ (L66078_EdenPool_Covid-DD-VIR-00207); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/81/4f7d3ab01d35df8434dede990722c9]
Jan-29 16:04:48.820 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.820 [Task submitter] INFO  nextflow.Session - [24/b4bee7] Submitted process > CAT_FASTQ (L66085_EdenPool_Covid-DD-VIR-00215)
Jan-29 16:04:48.824 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: CAT_FASTQ (L66090_EdenPool_Covid-DD-VIR-00226); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/35/b68bc5ca082cac0a2dfeb834217ea3]
Jan-29 16:04:48.828 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.828 [Task submitter] INFO  nextflow.Session - [19/8f7b2e] Submitted process > CAT_FASTQ (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06)
Jan-29 16:04:48.832 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: CAT_FASTQ (L66094_EdenPool_Covid-DD-VIR-00236); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/21/f7ef2cc87ae61f24496d13329203b5]
Jan-29 16:04:48.839 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.839 [Task submitter] INFO  nextflow.Session - [97/1600e2] Submitted process > CAT_FASTQ (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06)
Jan-29 16:04:48.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: MAKE_SNPEFF_DB (GCA_009858895.3_ASM985889v3_genomic.200409.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/22/49fc18a973328f28a8ba8c964c0f62]
Jan-29 16:04:48.912 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: CAT_FASTQ (L66088_EdenPool_Covid-DD-VIR-00221); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fc/9de7d19fa9899b1018ed7f9c130d08]
Jan-29 16:04:48.913 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.914 [Task submitter] INFO  nextflow.Session - [ac/a64d0e] Submitted process > CAT_FASTQ (L66096_EdenPool_Covid-DD-VIR-00238)
Jan-29 16:04:48.921 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.921 [Task submitter] INFO  nextflow.Session - [e2/db0d35] Submitted process > CAT_FASTQ (L66102_EdenPool_Covid-DD-VIR-00246)
Jan-29 16:04:48.927 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.927 [Task submitter] INFO  nextflow.Session - [98/f973c4] Submitted process > CAT_FASTQ (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01)
Jan-29 16:04:48.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: CAT_FASTQ (L66097_EdenPool_Covid-DD-VIR-00240); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8c/eb1e125072237010566b835ef69cf8]
Jan-29 16:04:48.975 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.975 [Task submitter] INFO  nextflow.Session - [3a/4085ea] Submitted process > CAT_FASTQ (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01)
Jan-29 16:04:49.170 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: CAT_FASTQ (L66077_EdenPool_Covid-DD-VIR-00206); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/15/592959d487540f1fcfc692d9df55e9]
Jan-29 16:04:49.174 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.174 [Task submitter] INFO  nextflow.Session - [38/92454e] Submitted process > CAT_FASTQ (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01)
Jan-29 16:04:49.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: CAT_FASTQ (L66076_EdenPool_Covid-DD-VIR-00205); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/96/91d0cf4dde4d86b574f632b32d9d16]
Jan-29 16:04:49.185 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.185 [Task submitter] INFO  nextflow.Session - [13/473b1a] Submitted process > CAT_FASTQ (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01)
Jan-29 16:04:49.308 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: CAT_FASTQ (L66079_EdenPool_Covid-DD-VIR-00208); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9c/76507b682b4350379f34c3fed7195d]
Jan-29 16:04:49.311 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.311 [Task submitter] INFO  nextflow.Session - [c9/699aeb] Submitted process > CAT_FASTQ (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01)
Jan-29 16:04:49.341 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: CAT_FASTQ (L66098_EdenPool_Covid-DD-VIR-00241); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9a/86c6865743e7dc7b5f3ea393164f62]
Jan-29 16:04:49.343 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.343 [Task submitter] INFO  nextflow.Session - [6c/486b0a] Submitted process > CAT_FASTQ (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01)
Jan-29 16:04:49.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: CAT_FASTQ (L66081_EdenPool_Covid-DD-VIR-00210); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/1fbe2088e24fcf2d8d71bcb4216027]
Jan-29 16:04:49.356 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.356 [Task submitter] INFO  nextflow.Session - [ee/e1ae84] Submitted process > CAT_FASTQ (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01)
Jan-29 16:04:49.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: CAT_FASTQ (L66092_EdenPool_Covid-DD-VIR-00231); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e5/7db6cd3ae948f35c8426a4892d9b19]
Jan-29 16:04:49.526 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.526 [Task submitter] INFO  nextflow.Session - [6c/67207e] Submitted process > CAT_FASTQ (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01)
Jan-29 16:04:49.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: CAT_FASTQ (L66074_EdenPool_Covid-DD-VIR-00201); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/81/23ed7411e836ceb3f47e131a72f506]
Jan-29 16:04:49.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: CAT_FASTQ (L66101_EdenPool_Covid-DD-VIR-00245); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a4/5d0aa31e8e2a2a1c41d55d325eb433]
Jan-29 16:04:49.541 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.541 [Task submitter] INFO  nextflow.Session - [4f/5893ff] Submitted process > CAT_FASTQ (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02)
Jan-29 16:04:49.545 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.545 [Task submitter] INFO  nextflow.Session - [09/68b04a] Submitted process > CAT_FASTQ (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02)
Jan-29 16:04:49.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: CAT_FASTQ (L66087_EdenPool_Covid-DD-VIR-00219); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b0/e41d544e0ae93b3b1a13948a0fa86c]
Jan-29 16:04:49.600 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.600 [Task submitter] INFO  nextflow.Session - [03/d660b8] Submitted process > CAT_FASTQ (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02)
Jan-29 16:04:49.684 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: CAT_FASTQ (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/97/1600e2676fd9a3bd5bd5c78bf8e2ca]
Jan-29 16:04:49.690 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.691 [Task submitter] INFO  nextflow.Session - [41/56446c] Submitted process > CAT_FASTQ (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02)
Jan-29 16:04:49.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: CAT_FASTQ (L66085_EdenPool_Covid-DD-VIR-00215); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/24/b4bee76330bb6c1266aec7a46cb40d]
Jan-29 16:04:49.768 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.769 [Task submitter] INFO  nextflow.Session - [fe/7bfe33] Submitted process > CAT_FASTQ (L66116_EdenPool_cDNA_S13_20210108-720393_01_E02)
Jan-29 16:04:49.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: CAT_FASTQ (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/19/8f7b2e585d49d0d23342cc1da5ad71]
Jan-29 16:04:49.820 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.820 [Task submitter] INFO  nextflow.Session - [80/b9b465] Submitted process > CAT_FASTQ (L66117_EdenPool_cDNA_S14_20210104-795197_01_F02)
Jan-29 16:04:49.821 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: CAT_FASTQ (L66096_EdenPool_Covid-DD-VIR-00238); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ac/a64d0e124058f4106ca369069c6f3d]
Jan-29 16:04:49.828 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.828 [Task submitter] INFO  nextflow.Session - [2e/e8da82] Submitted process > CAT_FASTQ (L66118_EdenPool_cDNA_S15_20210104-794211_01_G02)
Jan-29 16:04:49.861 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: CAT_FASTQ (L66102_EdenPool_Covid-DD-VIR-00246); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e2/db0d35b8d6a044b4960e78d7ee7d77]
Jan-29 16:04:49.865 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.865 [Task submitter] INFO  nextflow.Session - [fa/684ec6] Submitted process > CAT_FASTQ (L66119_EdenPool_cDNA_S16_20210104-794508_01_H02)
Jan-29 16:04:49.976 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: CAT_FASTQ (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/98/f973c416041bf56ec445e28726a069]
Jan-29 16:04:49.979 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.979 [Task submitter] INFO  nextflow.Session - [07/869e09] Submitted process > CAT_FASTQ (L66120_EdenPool_cDNA_S17_20210105-796034_01_A03)
Jan-29 16:04:50.076 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: CAT_FASTQ (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3a/4085ea0836ae79dfe1c111c2e8d755]
Jan-29 16:04:50.080 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.080 [Task submitter] INFO  nextflow.Session - [3f/d866ed] Submitted process > CAT_FASTQ (L66121_EdenPool_cDNA_S18_20210105-796550_01_B03)
Jan-29 16:04:50.120 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: CAT_FASTQ (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/92454ea4b5231b19b684b3921d9c9b]
Jan-29 16:04:50.123 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.123 [Task submitter] INFO  nextflow.Session - [6c/d366b6] Submitted process > CAT_FASTQ (L66122_EdenPool_cDNA_S19_20210106-797851_01_C03)
Jan-29 16:04:50.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: CAT_FASTQ (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/13/473b1aed59cb54dc087c438fcb6dfb]
Jan-29 16:04:50.128 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.128 [Task submitter] INFO  nextflow.Session - [14/24e7bd] Submitted process > CAT_FASTQ (L66123_EdenPool_cDNA_S20_20210103-793929_01_D03)
Jan-29 16:04:50.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: CAT_FASTQ (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/486b0aff6c030480268baaf8fe9f5f]
Jan-29 16:04:50.166 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.167 [Task submitter] INFO  nextflow.Session - [c0/43a774] Submitted process > CAT_FASTQ (L66124_EdenPool_cDNA_S21_20210103-793393_01_E03)
Jan-29 16:04:50.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: CAT_FASTQ (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/699aeb8603c2812b655bd57ff95c49]
Jan-29 16:04:50.200 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.200 [Task submitter] INFO  nextflow.Session - [9d/5e0847] Submitted process > CAT_FASTQ (L66125_EdenPool_cDNA_S22_20210103-793390_01_F03)
Jan-29 16:04:50.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: CAT_FASTQ (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ee/e1ae8489bd48a0e79b3e2843e15c91]
Jan-29 16:04:50.341 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.341 [Task submitter] INFO  nextflow.Session - [b1/be8b52] Submitted process > CAT_FASTQ (L66126_EdenPool_cDNA_S23_20210103-793439_01_G03)
Jan-29 16:04:50.452 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: CAT_FASTQ (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4f/5893ff34ca2604897a89b20918db9c]
Jan-29 16:04:50.454 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.454 [Task submitter] INFO  nextflow.Session - [17/071bea] Submitted process > CAT_FASTQ (L66127_EdenPool_cDNA_S24_20210102-792782_01_H03)
Jan-29 16:04:50.484 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: CAT_FASTQ (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/67207e44eac9f050eb8e70be1f6054]
Jan-29 16:04:50.487 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.487 [Task submitter] INFO  nextflow.Session - [b2/91340c] Submitted process > CAT_FASTQ (L66128_EdenPool_cDNA_S25_20210101-792223_01_A04)
Jan-29 16:04:50.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: CAT_FASTQ (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/09/68b04ae1b388bc18c01a823327eaed]
Jan-29 16:04:50.584 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.585 [Task submitter] INFO  nextflow.Session - [76/c8f1e9] Submitted process > CAT_FASTQ (L66129_EdenPool_cDNA_S26_20201230-791215_01_B04)
Jan-29 16:04:50.586 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: CAT_FASTQ (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/03/d660b80221c6dcbe01ed75b36bf501]
Jan-29 16:04:50.590 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.590 [Task submitter] INFO  nextflow.Session - [bb/a4b504] Submitted process > CAT_FASTQ (L66130_EdenPool_cDNA_S27_20201230-790456_01_C04)
Jan-29 16:04:50.608 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: CAT_FASTQ (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/41/56446c28275b4e533aa15d00c3b587]
Jan-29 16:04:50.611 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.611 [Task submitter] INFO  nextflow.Session - [06/777eeb] Submitted process > CAT_FASTQ (L66131_EdenPool_cDNA_S28_20201230-790289_01_D04)
Jan-29 16:04:50.770 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: CAT_FASTQ (L66118_EdenPool_cDNA_S15_20210104-794211_01_G02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/2e/e8da822dda73c481c282b570bd1472]
Jan-29 16:04:50.773 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.773 [Task submitter] INFO  nextflow.Session - [09/d9e151] Submitted process > CAT_FASTQ (L66132_EdenPool_cDNA_S29_20201230-790328_01_E04)
Jan-29 16:04:50.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: CAT_FASTQ (L66116_EdenPool_cDNA_S13_20210108-720393_01_E02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fe/7bfe333ce9dc422811ebb230642f8d]
Jan-29 16:04:50.808 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.808 [Task submitter] INFO  nextflow.Session - [34/fb6bae] Submitted process > CAT_FASTQ (L66133_EdenPool_cDNA_S30_20201230-790469_01_F04)
Jan-29 16:04:50.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: CAT_FASTQ (L66119_EdenPool_cDNA_S16_20210104-794508_01_H02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fa/684ec6e9967ecdc9c8842ad4d7d37a]
Jan-29 16:04:50.816 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.816 [Task submitter] INFO  nextflow.Session - [72/0b7b4a] Submitted process > CAT_FASTQ (L66134_EdenPool_cDNA_S31_20201230-790388_01_G04)
Jan-29 16:04:50.968 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: CAT_FASTQ (L66117_EdenPool_cDNA_S14_20210104-795197_01_F02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/80/b9b46584d249056903b64f468881ce]
Jan-29 16:04:50.972 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.972 [Task submitter] INFO  nextflow.Session - [f4/662279] Submitted process > CAT_FASTQ (L66135_EdenPool_cDNA_S32_20201230-790275_01_H04)
Jan-29 16:04:50.996 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: CAT_FASTQ (L66120_EdenPool_cDNA_S17_20210105-796034_01_A03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/07/869e091f43a5b4c0bbba297fe0eb0f]
Jan-29 16:04:51.001 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.001 [Task submitter] INFO  nextflow.Session - [a0/7746cd] Submitted process > CAT_FASTQ (L66136_EdenPool_cDNA_S33_20201230-791165_01_A05)
Jan-29 16:04:51.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: CAT_FASTQ (L66121_EdenPool_cDNA_S18_20210105-796550_01_B03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/d866ed926d80550ae0e50ea5eec4fe]
Jan-29 16:04:51.125 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.125 [Task submitter] INFO  nextflow.Session - [d1/43fc04] Submitted process > CAT_FASTQ (L66137_EdenPool_cDNA_S34_20201229-789657_01_B05)
Jan-29 16:04:51.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: CAT_FASTQ (L66122_EdenPool_cDNA_S19_20210106-797851_01_C03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/d366b6ff4aca91634251e9d5b294cb]
Jan-29 16:04:51.291 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.291 [Task submitter] INFO  nextflow.Session - [3c/d49ad1] Submitted process > CAT_FASTQ (L66138_EdenPool_cDNA_S35_20201228-788665_01_C05)
Jan-29 16:04:51.344 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: CAT_FASTQ (L66124_EdenPool_cDNA_S21_20210103-793393_01_E03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c0/43a774ac84a96f18f39f465c19749e]
Jan-29 16:04:51.346 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.346 [Task submitter] INFO  nextflow.Session - [e1/b63762] Submitted process > CAT_FASTQ (L66139_EdenPool_cDNA_S36_20201228-788797_01_D05)
Jan-29 16:04:51.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: CAT_FASTQ (L66123_EdenPool_cDNA_S20_20210103-793929_01_D03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/14/24e7bdb4a1991f4a6bff51aa8edc0c]
Jan-29 16:04:51.390 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.390 [Task submitter] INFO  nextflow.Session - [12/424e0e] Submitted process > CAT_FASTQ (L66140_EdenPool_cDNA_S37_20201228-788712_01_E05)
Jan-29 16:04:51.421 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: CAT_FASTQ (L66125_EdenPool_cDNA_S22_20210103-793390_01_F03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9d/5e08477bbf93045cdfa858ee58bed9]
Jan-29 16:04:51.423 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.423 [Task submitter] INFO  nextflow.Session - [4a/5590a4] Submitted process > CAT_FASTQ (L66141_EdenPool_cDNA_S38_20201228-788358_01_F05)
Jan-29 16:04:51.500 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: CAT_FASTQ (L66126_EdenPool_cDNA_S23_20210103-793439_01_G03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b1/be8b52e7592f8c89c2f47f97c0b1c6]
Jan-29 16:04:51.505 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.505 [Task submitter] INFO  nextflow.Session - [ac/90e40a] Submitted process > CAT_FASTQ (L66142_EdenPool_cDNA_S39_20201228-788063_01_G05)
Jan-29 16:04:51.529 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: CAT_FASTQ (L66129_EdenPool_cDNA_S26_20201230-791215_01_B04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/76/c8f1e96eacc74e74a336836b7b5e72]
Jan-29 16:04:51.533 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.533 [Task submitter] INFO  nextflow.Session - [4d/c43fd3] Submitted process > CAT_FASTQ (L66143_EdenPool_cDNA_S40_20201228-787781_01_H05)
Jan-29 16:04:51.612 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: CAT_FASTQ (L66127_EdenPool_cDNA_S24_20210102-792782_01_H03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/17/071beac07e8ed046765cdfac48ec11]
Jan-29 16:04:51.614 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.614 [Task submitter] INFO  nextflow.Session - [79/3c3b41] Submitted process > CAT_FASTQ (L66146_EdenPool_cDNA_S43_20201227-787460_01_C06)
Jan-29 16:04:51.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: CAT_FASTQ (L66128_EdenPool_cDNA_S25_20210101-792223_01_A04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b2/91340cba5bc697ecf038adcf64c94f]
Jan-29 16:04:51.625 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.625 [Task submitter] INFO  nextflow.Session - [ea/13c5cd] Submitted process > CAT_FASTQ (L66147_EdenPool_cDNA_S44_20201226-787053_01_D06)
Jan-29 16:04:51.712 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: CAT_FASTQ (L66130_EdenPool_cDNA_S27_20201230-790456_01_C04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/bb/a4b50431fd7e3b4495b3dc4484ff2d]
Jan-29 16:04:51.715 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.715 [Task submitter] INFO  nextflow.Session - [e6/d017db] Submitted process > CAT_FASTQ (L66148_EdenPool_cDNA_S45_20210103-793417_01_E06)
Jan-29 16:04:51.897 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: CAT_FASTQ (L66131_EdenPool_cDNA_S28_20201230-790289_01_D04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/06/777eebea303557608d93be7ce982fa]
Jan-29 16:04:51.900 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.900 [Task submitter] INFO  nextflow.Session - [9c/1344e9] Submitted process > CAT_FASTQ (L66149_EdenPool_cDNA_S46_20210103-793617_01_F06)
Jan-29 16:04:51.948 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: CAT_FASTQ (L66133_EdenPool_cDNA_S30_20201230-790469_01_F04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/34/fb6baec0289e0b3725045a248600a9]
Jan-29 16:04:51.950 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.950 [Task submitter] INFO  nextflow.Session - [f8/bba5f8] Submitted process > CAT_FASTQ (L66150_EdenPool_cDNA_S47_20210103-793411_01_G06)
Jan-29 16:04:52.061 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: CAT_FASTQ (L66134_EdenPool_cDNA_S31_20201230-790388_01_G04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/72/0b7b4a90309edcb1c0194e38a8fcc3]
Jan-29 16:04:52.065 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.065 [Task submitter] INFO  nextflow.Session - [d4/cd8a88] Submitted process > CAT_FASTQ (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06)
Jan-29 16:04:52.068 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: CAT_FASTQ (L66135_EdenPool_cDNA_S32_20201230-790275_01_H04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f4/662279be13bc1ef173978f609794e5]
Jan-29 16:04:52.073 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.073 [Task submitter] INFO  nextflow.Session - [cf/1f2fc8] Submitted process > CAT_FASTQ (L66152_EdenPool_Covid-DD-VIR-00103)
Jan-29 16:04:52.089 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/99/ab7350c18e31255310114459b124bb]
Jan-29 16:04:52.093 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: CAT_FASTQ (L66132_EdenPool_cDNA_S29_20201230-790328_01_E04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/09/d9e15114e1459fa14a46ef7fc7eaed]
Jan-29 16:04:52.093 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.093 [Task submitter] INFO  nextflow.Session - [33/aa3b31] Submitted process > CAT_FASTQ (L66153_EdenPool_FH_0152)
Jan-29 16:04:52.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: CAT_FASTQ (L66136_EdenPool_cDNA_S33_20201230-791165_01_A05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a0/7746cda21070cfeb6fed4e05353473]
Jan-29 16:04:52.098 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.098 [Task submitter] INFO  nextflow.Session - [9f/d91a4c] Submitted process > CAT_FASTQ (L66154_EdenPool_FH_0170)
Jan-29 16:04:52.105 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.105 [Task submitter] INFO  nextflow.Session - [d7/2d078d] Submitted process > CAT_FASTQ (L66155_EdenPool_FH_0455)
Jan-29 16:04:52.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: CAT_FASTQ (L66138_EdenPool_cDNA_S35_20201228-788665_01_C05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3c/d49ad142687482d29992645cb56a0e]
Jan-29 16:04:52.257 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.257 [Task submitter] INFO  nextflow.Session - [8e/5a9863] Submitted process > CAT_FASTQ (L66156_EdenPool_FH_0769)
Jan-29 16:04:52.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: CAT_FASTQ (L66137_EdenPool_cDNA_S34_20201229-789657_01_B05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d1/43fc04b80fe00fcfe25cc33dd805b8]
Jan-29 16:04:52.340 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.341 [Task submitter] INFO  nextflow.Session - [75/ac8598] Submitted process > CAT_FASTQ (L66157_EdenPool_FH_0770)
Jan-29 16:04:52.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: CAT_FASTQ (L66139_EdenPool_cDNA_S36_20201228-788797_01_D05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e1/b63762e4f4dc53e2f9f43ef97424a4]
Jan-29 16:04:52.493 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.494 [Task submitter] INFO  nextflow.Session - [50/474db9] Submitted process > CAT_FASTQ (L66158_EdenPool_FH_0790)
Jan-29 16:04:52.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: CAT_FASTQ (L66141_EdenPool_cDNA_S38_20201228-788358_01_F05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4a/5590a4395b3018a9c04538ca18c2f9]
Jan-29 16:04:52.625 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.626 [Task submitter] INFO  nextflow.Session - [79/851e6d] Submitted process > CAT_FASTQ (L66159_EdenPool_Covid-DD-VIR-00247)
Jan-29 16:04:52.626 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: CAT_FASTQ (L66142_EdenPool_cDNA_S39_20201228-788063_01_G05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ac/90e40a1f35178f1e802356616f0917]
Jan-29 16:04:52.721 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: CAT_FASTQ (L66140_EdenPool_cDNA_S37_20201228-788712_01_E05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/12/424e0effc8a49be5aac16864a66e3d]
Jan-29 16:04:52.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: CAT_FASTQ (L66143_EdenPool_cDNA_S40_20201228-787781_01_H05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4d/c43fd32e0f2f749fd4b01ce15aa6f2]
Jan-29 16:04:52.773 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: CAT_FASTQ (L66146_EdenPool_cDNA_S43_20201227-787460_01_C06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/79/3c3b4148c68c5dde4a2b9b2d33502f]
Jan-29 16:04:52.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: CAT_FASTQ (L66147_EdenPool_cDNA_S44_20201226-787053_01_D06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ea/13c5cdd02ca360651d5b6de72820e4]
Jan-29 16:04:52.933 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: CAT_FASTQ (L66148_EdenPool_cDNA_S45_20210103-793417_01_E06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e6/d017db51f9a720c6dfc800cbc75314]
Jan-29 16:04:52.936 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.936 [Task submitter] INFO  nextflow.Session - [9b/70cee0] Submitted process > FASTQC (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:52.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: CAT_FASTQ (L66149_EdenPool_cDNA_S46_20210103-793617_01_F06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9c/1344e9d6f0cacc0131caa9fcf9e04b]
Jan-29 16:04:53.037 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: CAT_FASTQ (L66150_EdenPool_cDNA_S47_20210103-793411_01_G06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f8/bba5f80219b0f124fd0122b89660e9]
Jan-29 16:04:53.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: CAT_FASTQ (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d4/cd8a88a697a1c1d567219162f70be1]
Jan-29 16:04:53.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: CAT_FASTQ (L66152_EdenPool_Covid-DD-VIR-00103); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/cf/1f2fc85c66414ce28c5eb878f6a2a8]
Jan-29 16:04:53.266 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: CAT_FASTQ (L66153_EdenPool_FH_0152); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/33/aa3b319dc3166a54fe83826aee3754]
Jan-29 16:04:53.364 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: CAT_FASTQ (L66154_EdenPool_FH_0170); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9f/d91a4c3783006c6da9fd2b64ba8c03]
Jan-29 16:04:53.366 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:53.366 [Task submitter] INFO  nextflow.Session - [b9/9c83de] Submitted process > FASTP (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:53.448 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: CAT_FASTQ (L66155_EdenPool_FH_0455); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d7/2d078d47553332a8028a32e528991e]
Jan-29 16:04:53.455 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: CAT_FASTQ (L66156_EdenPool_FH_0769); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8e/5a9863bccaac2d59b67050f59999bb]
Jan-29 16:04:53.493 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: CAT_FASTQ (L66157_EdenPool_FH_0770); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/75/ac8598497ef7801737fb468b48ff7a]
Jan-29 16:04:53.609 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: CAT_FASTQ (L66158_EdenPool_FH_0790); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/50/474db92fd3d9b409f02d0aea6b4597]
Jan-29 16:04:53.676 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: CAT_FASTQ (L66159_EdenPool_Covid-DD-VIR-00247); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/79/851e6dbd68d3e21b855c0de399c578]
Jan-29 16:04:58.277 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: FASTQC (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9b/70cee026491c6b3868f42bf7b63f48]
Jan-29 16:04:58.285 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:58.285 [Task submitter] INFO  nextflow.Session - [72/7c6b51] Submitted process > FASTQC (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:05:03.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: FASTQC (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/72/7c6b518ac1f5250300a57eadb16d34]
Jan-29 16:05:03.205 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:03.206 [Task submitter] INFO  nextflow.Session - [41/32b6eb] Submitted process > FASTP (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:05:05.552 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: FASTP (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b9/9c83defbd8e71dbf0802bfcb1f8246]
Jan-29 16:05:05.557 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:05.557 [Task submitter] INFO  nextflow.Session - [c9/b3b26f] Submitted process > FASTQC (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:05:10.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: FASTQC (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/b3b26faee1218913255be20f92783a]
Jan-29 16:05:10.397 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:10.397 [Task submitter] INFO  nextflow.Session - [b0/3bd9ff] Submitted process > FASTP (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:05:11.357 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: FASTP (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/41/32b6ebc91a6e9c44e1d2a6227b5294]
Jan-29 16:05:11.361 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:11.361 [Task submitter] INFO  nextflow.Session - [77/15a96a] Submitted process > FASTQC (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:05:16.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: FASTQC (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/77/15a96a627858e29aa57ed4d737a670]
Jan-29 16:05:16.314 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:16.314 [Task submitter] INFO  nextflow.Session - [b9/73eb29] Submitted process > FASTP (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:05:18.521 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: FASTP (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b0/3bd9ffa974be35acb098e64e735915]
Jan-29 16:05:18.526 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:18.526 [Task submitter] INFO  nextflow.Session - [14/139f49] Submitted process > FASTP (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:05:25.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: FASTP (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/14/139f49a415a39389f105874bdd6ccd]
Jan-29 16:05:25.601 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:25.602 [Task submitter] INFO  nextflow.Session - [15/c9f701] Submitted process > FASTQC (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:05:26.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: FASTP (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b9/73eb295f19bd2702d3cba1138d4053]
Jan-29 16:05:26.605 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:26.605 [Task submitter] INFO  nextflow.Session - [c1/94a425] Submitted process > FASTQC (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:05:31.545 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: FASTQC (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/15/c9f701f860de8cb4bccaa5f620202e]
Jan-29 16:05:31.549 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:31.549 [Task submitter] INFO  nextflow.Session - [3f/9b4d47] Submitted process > FASTP (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:05:31.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: FASTQC (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c1/94a4258145cd345cc8545de512e5d5]
Jan-29 16:05:31.593 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:31.593 [Task submitter] INFO  nextflow.Session - [e4/f1464d] Submitted process > FASTQC (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:05:35.513 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: FASTQC (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e4/f1464d64eeba0abeb39754b6dcb871]
Jan-29 16:05:35.518 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:35.518 [Task submitter] INFO  nextflow.Session - [db/dfa667] Submitted process > FASTP (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:05:39.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: FASTP (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/9b4d477164f19c68dfde1fdba02f4f]
Jan-29 16:05:39.622 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:39.622 [Task submitter] INFO  nextflow.Session - [7d/08c5e8] Submitted process > FASTP (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:05:45.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: FASTP (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/db/dfa667a5de08f25b485aed706c4341]
Jan-29 16:05:45.585 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:45.585 [Task submitter] INFO  nextflow.Session - [69/7a513e] Submitted process > FASTQC (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:05:47.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: FASTP (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/7d/08c5e824285d6f441e629421060421]
Jan-29 16:05:47.621 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:47.622 [Task submitter] INFO  nextflow.Session - [43/666074] Submitted process > FASTQC (L66091_EdenPool_Covid-DD-VIR-00229)
Jan-29 16:05:50.605 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: FASTQC (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/69/7a513e68614cd5c9f90dc7ef873bfa]

Running with -profile test,singularity, I get:
-Warning, pipeline completed, but with errored process(es) -
-Number of ignored errored process(es) : 22 -
-Number of successfully ran process(es) : 120 -
-[nf-core/viralrecon] Pipeline completed successfully-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 29-Jan-2021 18:28:41
Duration    : 4m 51s
CPU hours   : 0.9 (12.2% failed)
Succeeded   : 120
Ignored     : 22
Failed      : 22

full log:
Jan-29 18:23:48.112 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon -profile test,singularity -r e49cee2
Jan-29 18:23:48.179 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.10.0
Jan-29 18:23:48.843 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 18:23:48.855 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 18:23:49.043 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/viralrecon` [crazy_ampere] - revision: e49cee2f15dce2e9993736d16f08b1f9d808e292
Jan-29 18:23:49.641 [main] DEBUG nextflow.scm.AssetManager - WARN: Cannot find any Git revision matching: null; ls-remote: [Ref[refs/pull/104/head=e21a9d69c8a80c902e8ed67ead97269ae040daa8], Ref[refs/pull/71/head=de556ff67b80ef002b437391fe3e8ae86ddfcca7], Ref[refs/pull/85/head=cea8613b4a939db7dc36fb639b0b05de07a9aaed], Ref[refs/tags/1.0.0=7422b0d353b1a295fb7cda47f2f7750c3bd890d1], Ref[refs/pull/69/head=b6e20251447dff08ea213605f4bfe554b17a0ab4], Ref[refs/pull/40/head=658104370a3aab1bde5e176750a1ae15687a0b89], Ref[refs/pull/24/head=b77d015ce4720e7447ee6c50fcca8758d16a173e], Ref[refs/pull/135/head=778693daee7a476c8cc9ed1b703bd0e801d42016], Ref[refs/pull/55/head=3bfc2ba5239baa54260a95f031523f4e212451f6], Ref[refs/heads/dsl2=c8f708819bede4b1c8f3840c6355c22b03e6d0e9], Ref[refs/pull/23/head=a87af4acb8a3afe26175da6feeb4c5ca28b3b436], Ref[refs/pull/148/head=9ba237e45aef44056dfd137caf33782252b8c9b2], Ref[refs/pull/120/head=4461c408701db0ba78264092632e45c93f83ba4c], Ref[refs/pull/103/head=372de46851a76d35c038fdf4a80d1207f71de073], Ref[refs/pull/68/head=487df0392fa1579abb9842d33111ebcc6e223d66], Ref[refs/pull/70/head=fb6596249daf33376ca148c6b06a9f2ebb50af8d], Ref[refs/pull/118/head=fb552abe4143334b8b6131028e029a6d9271202a], Ref[refs/pull/150/head=74e32eeb8efa98fea152899ae9e5f43f0aefe087], Ref[refs/pull/38/head=6030094912cb345c1b16584a713c0b94595003e0], Ref[refs/pull/134/head=abcd646b49cd7bccc8e8c4ddf164782731e1eb56], Ref[refs/pull/54/head=4c4103b9fda02bf60c8f77e424ab11d0b783e43e], Ref[refs/pull/99/head=6756a4e3a518e2cac416550168a6b89c57975785], Ref[refs/pull/98/head=afc1fd67c633482675226db3906f9e0ed93ab56f], Ref[refs/pull/84/head=52db59ea24b462f0760896bdeb2f743c85a8b781], Ref[refs/pull/11/head=886c2f681f33e75858deb6e9d1c914fdb299c035], Ref[refs/pull/39/head=0b12a3e4f87ca8f0f83fbde0737466268e15785c], Ref[refs/pull/87/head=d3c56f47a3a51a50a526590901e3f1bfe3db6049], Ref[refs/pull/116/head=e1134ed88cec082d6f7373ba96bfc4e0ecc412bc], Ref[refs/pull/119/head=43c9d78884774bfe5e419014c38cf1e8b31c6710], Ref[refs/pull/41/head=4853f86c0869171b16a53b767401a5a341167e53], Ref[refs/pull/36/head=3eaeb42a7b15701ec7107498e5cdd5866325143c], Ref[refs/pull/52/head=9e511349d7e899310a41fa9b46269571e39034f5], Ref[refs/pull/22/head=a580cfaa886907f4cda826088a15cc8241a99c31], Ref[refs/pull/102/head=1b93695f72a814764cc7dbf74d6a47855042b87a], Ref[refs/pull/25/head=6ebfb8a9d9c42dc06827211f6ef576bdee232efa], Ref[refs/pull/105/head=9a46ba7d317c00e23bdfb889dd1298c33171c99c], Ref[refs/pull/146/head=90079b0fa5d37ffd551c4a9a18cba4f9860a017b], Ref[refs/pull/49/head=fee3c68ef7053fc9bd79a11937320abd056f0948], Ref[refs/pull/88/head=00816d0ec217c4adc2fa38ea07ef882d4dd1c822], Ref[refs/tags/1.1.0=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/140/head=2898d227ba61e2920fc4cc36ed6e5cd14064b7f7], Ref[refs/pull/60/head=eaab9880c914ea28d55f9077005808b9034a60ab], Ref[refs/pull/18/head=23ef7e0cacaa1726777c2a00dd7d138948f99fe8], Ref[refs/pull/82/head=7f8c7988f95c339debce2b3570df0f399fc230e0], Ref[refs/pull/21/head=4a485b793c961d148fae1bbf7f202b49a28307a3], Ref[refs/pull/65/head=3d6512ac4e109958c5fbf719ccbbd14ed9004017], Ref[refs/pull/27/head=775379f647f9e2e41a0dee869dd31d9fef06a9df], Ref[refs/pull/145/head=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/pull/43/head=2e5a2b4772239651bd292cbdd1d21fc69c4d1caa], Ref[refs/pull/129/head=7b38fe2439f97927093452232263123e71368d44], Ref[refs/pull/59/head=046d91a78b5c112a93ed7ef7d185c18a19bea8b9], Ref[refs/pull/139/head=60cd93051c5de0af9f79886e48d7c96c6b4ae199], Ref[refs/pull/53/head=ac36d1fcf11674ab8ccf8b77a7bfb414614b9cad], Ref[refs/pull/111/head=69326f97b1c1d1b8733a0df573cb1f3eff907e6d], Ref[refs/pull/136/head=7002a5eb6f481075cf577e7898212bf01144e2f9], Ref[refs/pull/130/head=b0229bbbc6eda0614aa40269a3f06b4edf78c360], Ref[refs/pull/117/head=acfc523f35cb9174c383b01cede82a14c8818688], Ref[refs/pull/133/head=52a1e50ff57cf2295e2de9b425f73f276f20bade], Ref[refs/pull/37/head=55c2a56f7101f4d9bc74fa91cbc6bf9fd81527e2], Ref[refs/pull/114/head=d0e3e179d14b95eb8a1b08c3edcea5012e741206], Ref[refs/pull/34/head=dad04235f8b75dabd385a2e2476a895629549d98], Ref[refs/pull/50/head=fc6eb38364aa85181defa21fb32ba9c56b87bd80], Ref[refs/pull/72/head=3c810f848c21ca58d69aa31b0cecb68889cecebd], Ref[refs/pull/97/head=c6682e57fd58b9ed743e388999c393f2cdaccd78], Ref[refs/pull/78/head=7c38d49a99fd897ac473995c29876c5579e1722d], Ref[refs/pull/91/head=b0f9b52f9d17ba097a518b4dd01e25da52c6159a], Ref[refs/pull/75/head=f9b4b596671b2325011c42734b14239027d62c1d], Ref[refs/pull/94/head=f7004dd083f523674b0b5b7b3d98176b8887b43e], Ref[refs/pull/32/head=cb10b45cadedd90d5da6460704d5cd5f15764c01], Ref[refs/pull/77/head=ed2511444ce83e7924e9fd91584c268251bb2e31], Ref[refs/pull/63/head=4f56a2b91f580fc4f1ff4ff9510bd675b1d512b0], Ref[refs/pull/29/head=634bf562df7712e80ffa57839263273a53b3ae6b], Ref[refs/pull/16/head=79005a50623da53a812584537ee081744631dbe2], Ref[refs/pull/93/head=a495c1c40bd21085c21247ad812e51bcbb90088f], Ref[refs/pull/76/head=8b7285dbb0baa5ee300a43500dbeff782b284134], Ref[refs/pull/15/head=f899da38519e283a12df70fa6f20efd0a851f053], Ref[refs/pull/126/head=13331866195d9b0cc0aee95fc0df881965be7ef3], Ref[refs/pull/62/head=edb5bd0b6f40ac15432d5d234293d39334fd347f], Ref[refs/pull/92/head=ecc1fdcf1dade61baa2f65c2904f88457aa54054], Ref[refs/pull/28/head=c83b9a771430ed9c793e78f4507b6ba50858950b], Ref[refs/pull/81/head=9b4444fc1bb6ea038245dcb57db55ff96161d977], Ref[refs/pull/79/head=d9ad5b9c6f6ee7e1c2e62c36d8df2ef13eecffc1], Ref[refs/pull/44/head=a6524572ebfc9a9b73b1c207d7b56f3c0c37a411], Ref[refs/pull/110/head=9ea4c1a52a0b55beb8fda28d9d5d318c7909a99c], Ref[refs/pull/7/head=053508707e945f883dd611cb6eab89be73f77f56], Ref[refs/pull/127/head=0a7325e0a42b5f06afcb622c74962a3899157eca], Ref[refs/pull/108/head=2622959ec0ca9753ccf35fb57fa38d12a688a4f2], Ref[refs/pull/30/head=8940416aacf0648eeef5fd083cc7cc333d266be4], Ref[refs/pull/17/head=747296441fb64b4bd1137fd8d93f08f91572f90b], Ref[refs/pull/74/head=72d240b1e367193672c4e8914ffd7d51c93fa39b], Ref[HEAD=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/35/head=3781ff8ee824eb0c63644145a48e45221e22de9a], Ref[refs/pull/132/head=5b355cd205b4fa66a6658500d3080481d02bc736], Ref[refs/pull/90/head=b2eef6ca9038df66be27c985372ca1125fc3d8a7], Ref[refs/pull/58/head=5d42f5891d40e249a27a5cc1dcff8e9c13ce78af], Ref[refs/pull/131/head=30db7f95649e6e4f309067f3acb15b86c4499c6d], Ref[refs/pull/20/head=5c7bd7013a253a9785b346f65cf9bfc898da48f6], Ref[refs/pull/137/head=ee5b7b7a47ddabc6b44ef203ce13599ed3e42079], Ref[refs/pull/51/head=6cc01895b3db2901ac33dad5ae2317664467ae35], Ref[refs/pull/19/head=29d89516b218140ce2a5ed4f04c7898d436fc390], Ref[refs/pull/100/head=85f13dd3df92feec87fbe5b367715bb53743067c], Ref[refs/pull/73/head=d07af1ccde076f7010330c1fdd7d60a7b4c6f5be], Ref[refs/pull/96/head=2d5cdb3d8234e7f11c079fe57d8b131010423aae], Ref[refs/pull/57/head=d72c512df8fd38215b8c9bc259a2b97373536ad0], Ref[refs/pull/125/head=c9d40fb3c3f0bf413d593d43c6483f0eca234249], Ref[refs/pull/128/head=eca1bdcdaed5aefaf74402c858a45dc1ba4d123a], Ref[refs/pull/64/head=f27a55065c359cc6f19c4ea8bd7b6d93375a8141], Ref[refs/pull/48/head=e0474ce0f9f7c198f5e49070536b76c70e4b2e0b], Ref[refs/pull/45/head=0687ec1ef98f3ae80c147329c193338d79f537d6], Ref[refs/pull/106/head=160438169ebb0e488fd75f4706dc6fb66888cd7f], Ref[refs/pull/109/head=a5c12fcbbe4ead170ccd13d54b2038406757f271], Ref[refs/heads/TEMPLATE=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/heads/dev=e49cee2f15dce2e9993736d16f08b1f9d808e292], Ref[refs/pull/83/head=d9589698b6189d60f996fc722d566f84c28215c2], Ref[refs/pull/86/head=5ac0f286bc4acf243ba7ea53a665fe24ab02f85b], Ref[refs/pull/141/head=052e9a8cdaa1260a6007571b97acc855b7513086], Ref[refs/pull/131/merge=103c74d77174b79e1060b5757209a016c1e26aa6], Ref[refs/heads/master=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/80/head=80a8eb55a94c26d7c488cf0290ff3dc904c3c42d], Ref[refs/pull/89/head=397f25529d0ca506666c88d74a5382fcbbbb481e], Ref[refs/pull/144/head=b006a4187540d86a80981d28c364779ffb2c4aeb], Ref[refs/pull/147/head=80b17e725ec72e03ee63be69187b0f2feb7e8ada]]
Jan-29 18:23:49.667 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.668 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.673 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,singularity`
...skipping...