2 correction steps

Hi,
Are the following commands correct set up for 2 correction steps?
minimap -Sw5 -L100 -m0 \
        -t 18 \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        | gzip -1 > Fruit.paf.gz

miniasm -f /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        Fruit.paf.gz \
        > Fruit.gfa

awk '{print ">"$2; print $3}' Fruit | fold  Fruit.gfa.fasta

# Correction 1

minimap Fruit.gfa.fasta \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        > Fruit.gfa1.paf

racon -t 18 \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        Fruit.gfa1.paf \
        Fruit.gfa.fasta \
        Fruit.racon1.fasta

# Correction 2

minimap Fruit.racon1.fasta \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        > Fruit.gfa2.paf

racon -t 18 \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        Fruit.gfa2.paf \
        Fruit.racon1.fasta \
        Fruit.racon2.fasta

Thank you in advance.
Michal

Hello Michal,
the commands look fine to me. Did you encounter any problems while running those?
Best regards,
Robert

Thank you. No, is still running.

I have got Segmentation fault in miniasm
[M::main::157984.585*12.95] loaded/built the index for 554680 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 121
[M::mm_idx_gen::166745.493*12.79] collected minimizers
[M::mm_idx_gen::166748.851*12.79] sorted minimizers
[M::main::166748.851*12.79] loaded/built the index for 227356 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 63
[M::main] Version: 0.2-r123
[M::main] CMD: minimap -Sw5 -L100 -m0 -t 18 /work/waterhouse_team/All_RawData/RSnSeQ_110Fruit.fastq /work/waterhouse_team/All_RawData/RSnSeQ_110Fruit.fastq
[M::main] Real time: 171546.589 sec; CPU: 2179553.276 sec
[M::main] ===> Step 1: reading read mappings <===
/var/spool/PBS/mom_priv/jobs/1708901.pbs.SC: line 24: 154671 Segmentation fault      miniasm -f /work/waterhouse_team/All_RawData/RSnSeQ_110Fruit.fastq Fruit.paf.gz > Fruit.gfa

Any idea what could cause it?
Best wishes,
Michal

The only thing that comes to my mind is that you don't have enough RAM. How large is the overlaps file (Fruit.paf.gz) and how much RAM is in your machine?
Best regards,
Robert

Fruit.paf.gz has a file size of 578Gb. It was running with 200GB of RAM.

Try running miniasm with parameters "-Rc2", but I doubt that the prefiltered overlaps will fit into 200GB.

I use miniasm 0.2-r128 and it does not have the R option.
> miniasm
Usage: miniasm [options] <in.paf>
Options:
  Pre-selection:
    -m INT      min match length [100]
    -i FLOAT    min identity [0.05]
    -s INT      min span [2000]
    -c INT      min coverage [3]
  Overlap:
    -o INT      min overlap [same as -s]
    -h INT      max over hang length [1000]
    -I FLOAT    min end-to-end match ratio [0.8]
  Layout:
    -g INT      max gap differences between reads for trans-reduction [1000]
    -d INT      max distance for bubble popping [50000]
    -e INT      small unitig threshold [4]
    -f FILE     read sequences []
    -n INT      rounds of short overlap removal [3]
    -r FLOAT[,FLOAT]
                max and min overlap drop ratio [0.7,0.5]
    -F FLOAT    aggressive overlap drop ratio in the end [0.8]
  Miscellaneous:
    -p STR      output information: bed, paf, sg or ug [ug]
    -b          both directions of an arc are present in input
    -1          skip 1-pass read selection
    -2          skip 2-pass read selection
    -V          print version number

See miniasm.1 for detailed description of the command-line options.

How much memory do you think it is required?
Thank you in advance.
Michal

As I recall, miniasm reads all overlaps into memory at once. You can try and use the latest version with parameter "-R". In addition, rename reads in "RSnSeQ_110Fruit.fastq" with ID-s (0, 1, 2, ...) and run minimap again. It will decrease the "Fruit.paf" file as it contains read names as strings, but this is not a guarantee that the overlaps will fit into memory.
Best regards,
Robert

Hi,
I ran miniasm -f /scratch/Fruit-data/RSnSeQ_110Fruit.fastq Fruit.paf.gz > Fruit.gfa  on 1 Tb machine, but it crashed at 537.9041 GB.
ubuntu@waterhouse-1:/scratch/racon$ /usr/bin/time -v sh racon.sh
[M::main] ===> Step 1: reading read mappings <===
Segmentation fault
fold: Fruit.gfa.fasta: No such file or directory
awk: cannot open Fruit (No such file or directory)
Segmentation fault
[Fri, 10 Mar 17 19:42:03 +0000 FATAL] #2: Could not open file. File path: 'Fruit.gfa.fasta'.In function: 'OpenFileForBatchLoading'.

[Fri, 10 Mar 17 19:42:03 +0000 FATAL] #2: Could not open file. File path: 'Fruit.gfa.fasta'.In function: 'OpenFileForBatchLoading'.
Exiting.
Segmentation fault
[Fri, 10 Mar 17 19:42:03 +0000 FATAL] #2: Could not open file. File path: 'Fruit.racon1.fasta'.In function: 'OpenFileForBatchLoading'.

[Fri, 10 Mar 17 19:42:03 +0000 FATAL] #2: Could not open file. File path: 'Fruit.racon1.fasta'.In function: 'OpenFileForBatchLoading'.
Exiting.
        Command being timed: "sh racon.sh"
        User time (seconds): 33721.26
        System time (seconds): 19289.04
        Percent of CPU this job got: 84%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 17:31:21
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 537904100
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 2
        Minor (reclaiming a frame) page faults: 38958619
        Voluntary context switches: 150183
        Involuntary context switches: 278050
        Swaps: 0
        File system inputs: 608231024
        File system outputs: 8
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

Thank you in advance.
Michal

Hi Michal,
I do not know what causes your error as miniasm is not a tool I wrote. Could you upload your read set and provide me the download link? I can try and help you when I get the data you try to assemble.
Best regards,
Robert

Thank you four your solution for miniasm. Unfortunately, I have got a new segmentation fault in minimap.
[M::mm_idx_gen::34.770*1.54] collected minimizers
[M::mm_idx_gen::41.440*1.77] sorted minimizers
[M::main::41.440*1.77] loaded/built the index for 250197 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 114
[M::main] Version: 0.2-r123
[M::main] CMD: minimap Fruit.gfa.fasta /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq
[M::main] Real time: 7129.032 sec; CPU: 23291.340 sec
/var/spool/PBS/mom_priv/jobs/1782678.pbs.SC: line 40:  4859 Illegal instruction     racon -t 18 /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq Fruit.gfa1.paf Fruit.gfa.fasta Fruit.racon1.fasta
/var/spool/PBS/mom_priv/jobs/1782678.pbs.SC: line 46:  4860 Segmentation fault      minimap Fruit.racon1.fasta /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq > Fruit.gfa2.paf
/var/spool/PBS/mom_priv/jobs/1782678.pbs.SC: line 53:  4861 Illegal instruction     racon -t 18 /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq Fruit.gfa2.paf Fruit.racon1.fasta Fruit.racon2.fasta

Please find below the updated workflow:
#!/bin/bash -l
#PBS -N racon
#PBS -j oe
#PBS -l walltime=150:00:00
#PBS -l mem=900G
#PBS -l ncpus=18
###PBS -M email@host

cd $PBS_O_WORKDIR

# http://inf-biox121.readthedocs.io/en/2016/Assembly/practicals/07_Assembly_using_minasm+racon.html

#minimap -Sw5 -L100 -m0 \
#       -t 18 \
#       /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
#       /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
#       | gzip -1 > Fruit.paf.gz

#miniasm -Rc2 -f /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
#       Fruit.paf.gz \
#       > Fruit.gfa

awk '{print ">"$2; print $3}' Fruit.gfa | fold >  Fruit.gfa.fasta

# Correction 1

minimap Fruit.gfa.fasta \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        > Fruit.gfa1.paf

racon -t 18 \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        Fruit.gfa1.paf \
        Fruit.gfa.fasta \
        Fruit.racon1.fasta

# Correction 2

minimap Fruit.racon1.fasta \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        > Fruit.gfa2.paf

racon -t 18 \
        /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq \
        Fruit.gfa2.paf \
        Fruit.racon1.fasta \
        Fruit.racon2.fasta

What did I miss?
Thank you in advance.
Michal

Hello Michal,
minimap segfaults due to missing input file 'Fruit.racon1.fasta'. The file is not created because Racon was not run at all, i.e. it exits with an error as well (illegal instruction). My guess is that your Racon executable was not created on the machine you are running your pipeline. Try a fresh install, or recompile Racon, and run your script again.
Best regards,
Robert

Hi Robert, I used bioconda package. I'll to compile it by myself. Do you think the above commands were correct?

Hi Michal, the commands look fine to me.

Hi,
I did git clone https://github.com/isovic/racon.git  && cd racon && make modules && make tools && make -j  and then added the bin folder into my .bashrc.
Unfortunately, I still got segmantion fault.
What could I have done wrong?
Thank you in advance.
Michal

Try running 'example1_1-paf-lambda-align.sh' from Racon root folder and send me the error report.
Best regards,
Robert

Hi, Please find the below the output from example1_1-paf-lambda-align.sh.
mkdir -p ./bin/
g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/racon ./obj_linux/codebase/spoa/src/sisd_alignment.o ./obj_linux/codebase/spoa/src/edge.o ./obj_linux/codebase/spoa/src/simd_alignment.o ./obj_linux/codebase/spoa/src/alignment.o ./obj_linux/codebase/spoa/src/node.o ./obj_linux/codebase/spoa/src/graph.o ./obj_linux/codebase/spoa/src/main.o ./obj_linux/codebase/spoa/src/spoa.o ./obj_linux/codebase/spoa/src/chain.o ./obj_linux/codebase/argparser/src/example.o ./obj_linux/codebase/argparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/consensus/pileup.o ./obj_linux/src/consensus/tictoc.o ./obj_linux/src/consensus/consensus_sam.o ./obj_linux/src/consensus/consensus_overlap.o ./obj_linux/src/main.o ./obj_linux/src/mhap.o -lpthread -lgomp -lm -lz
/usr/bin/ld: skipping incompatible /usr/lib/../lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/../lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/../lib/libc.so when searching for -lc
tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter0.fasta test-data/lambda/reads.fastq.fasta > results/temp/consensus-lambda_30x_ont-paf-align-iter1.paf
[M::mm_idx_gen::0.106*0.04] collected minimizers
[M::mm_idx_gen::0.109*0.04] sorted minimizers
[M::main::0.109*0.04] loaded/built the index for 1 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 2
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter0.fasta test-data/lambda/reads.fastq.fasta
[M::main] Real time: 0.143 sec; CPU: 0.056 sec
test-data/lambda/reads.fastq

Running Racon:
    bin/racon -M 5 -X -4 -G -8 -E -6 --bq 10 -t 1 test-data/lambda/reads.fastq results/temp/consensus-lambda_30x_ont-paf-align-iter1.paf results/consensus-lambda_30x_ont-paf-align-iter0.fasta results/consensus-lambda_30x_ont-paf-align-iter1.fasta
[19:24:49 main] Using PAF for input alignments. (results/temp/consensus-lambda_30x_ont-paf-align-iter1.paf)
[19:24:49 main] Loading reads.
[19:24:49 main] Hashing qnames.
[19:24:49 main] Parsing the overlaps file.
[19:24:49 main] Unique overlaps will be filtered on the fly.
[19:24:49 main] Overlaps will be fully aligned.
[19:24:49 ConsensusFromOverlaps] Running consensus.
[19:24:49 ConsensusFromOverlaps] Separating overlaps to individual contigs.
[19:24:49 ConsensusFromOverlaps] In total, there are 1 contigs for consensus, each containing:
[19:24:49 ConsensusFromOverlaps] 	[0] utg000001l 186 alignments, contig len: 47161

[19:24:49 ConsensusFromOverlaps] Started processing contig 1 / 1 (100.00%): utg000001l
[19:24:49 ConsensusFromOverlaps] (thread_id = 0) Aligning overlaps for contig 1 / 1 (100.00%): utg000001l

[19:24:49 AlignOverlaps] Aligning overlap: 0 / 185 (0.54%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 1 / 185 (1.08%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 2 / 185 (1.62%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 3 / 185 (2.16%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 4 / 185 (2.70%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 5 / 185 (3.24%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 6 / 185 (3.78%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 7 / 185 (4.32%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 8 / 185 (4.86%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 9 / 185 (5.41%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 10 / 185 (5.95%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 11 / 185 (6.49%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 12 / 185 (7.03%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 13 / 185 (7.57%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 14 / 185 (8.11%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 15 / 185 (8.65%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 16 / 185 (9.19%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 17 / 185 (9.73%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 18 / 185 (10.27%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 19 / 185 (10.81%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 20 / 185 (11.35%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 21 / 185 (11.89%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 22 / 185 (12.43%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 23 / 185 (12.97%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 24 / 185 (13.51%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 25 / 185 (14.05%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 26 / 185 (14.59%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 27 / 185 (15.14%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 28 / 185 (15.68%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 29 / 185 (16.22%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 30 / 185 (16.76%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 31 / 185 (17.30%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 32 / 185 (17.84%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 33 / 185 (18.38%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 34 / 185 (18.92%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 35 / 185 (19.46%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 36 / 185 (20.00%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 37 / 185 (20.54%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 38 / 185 (21.08%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 39 / 185 (21.62%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 40 / 185 (22.16%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 41 / 185 (22.70%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 42 / 185 (23.24%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 43 / 185 (23.78%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 44 / 185 (24.32%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 45 / 185 (24.86%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 46 / 185 (25.41%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 47 / 185 (25.95%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 48 / 185 (26.49%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 49 / 185 (27.03%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 50 / 185 (27.57%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 51 / 185 (28.11%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 52 / 185 (28.65%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 53 / 185 (29.19%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 54 / 185 (29.73%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 55 / 185 (30.27%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 56 / 185 (30.81%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 57 / 185 (31.35%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 58 / 185 (31.89%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 59 / 185 (32.43%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 60 / 185 (32.97%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 61 / 185 (33.51%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 62 / 185 (34.05%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 63 / 185 (34.59%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 64 / 185 (35.14%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 65 / 185 (35.68%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 66 / 185 (36.22%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 67 / 185 (36.76%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 68 / 185 (37.30%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 69 / 185 (37.84%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 70 / 185 (38.38%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 71 / 185 (38.92%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 72 / 185 (39.46%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 73 / 185 (40.00%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 74 / 185 (40.54%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 75 / 185 (41.08%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 76 / 185 (41.62%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 77 / 185 (42.16%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 78 / 185 (42.70%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 79 / 185 (43.24%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 80 / 185 (43.78%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 81 / 185 (44.32%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 82 / 185 (44.86%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 83 / 185 (45.41%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 84 / 185 (45.95%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 85 / 185 (46.49%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 86 / 185 (47.03%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 87 / 185 (47.57%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 88 / 185 (48.11%), skipped 0 / 185 (0.00%)
[19:24:49 AlignOverlaps] Aligning overlap: 89 / 185 (48.65%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 90 / 185 (49.19%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 91 / 185 (49.73%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 92 / 185 (50.27%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 93 / 185 (50.81%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 94 / 185 (51.35%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 95 / 185 (51.89%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 96 / 185 (52.43%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 97 / 185 (52.97%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 98 / 185 (53.51%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 99 / 185 (54.05%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 100 / 185 (54.59%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 101 / 185 (55.14%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 102 / 185 (55.68%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 103 / 185 (56.22%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 104 / 185 (56.76%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 105 / 185 (57.30%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 106 / 185 (57.84%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 107 / 185 (58.38%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 108 / 185 (58.92%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 109 / 185 (59.46%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 110 / 185 (60.00%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 111 / 185 (60.54%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 112 / 185 (61.08%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 113 / 185 (61.62%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 114 / 185 (62.16%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 115 / 185 (62.70%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 116 / 185 (63.24%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 117 / 185 (63.78%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 118 / 185 (64.32%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 119 / 185 (64.86%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 120 / 185 (65.41%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 121 / 185 (65.95%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 122 / 185 (66.49%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 123 / 185 (67.03%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 124 / 185 (67.57%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 125 / 185 (68.11%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 126 / 185 (68.65%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 127 / 185 (69.19%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 128 / 185 (69.73%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 129 / 185 (70.27%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 130 / 185 (70.81%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 131 / 185 (71.35%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 132 / 185 (71.89%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 133 / 185 (72.43%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 134 / 185 (72.97%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 135 / 185 (73.51%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 136 / 185 (74.05%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 137 / 185 (74.59%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 138 / 185 (75.14%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 139 / 185 (75.68%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 140 / 185 (76.22%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 141 / 185 (76.76%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 142 / 185 (77.30%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 143 / 185 (77.84%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 144 / 185 (78.38%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 145 / 185 (78.92%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 146 / 185 (79.46%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 147 / 185 (80.00%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 148 / 185 (80.54%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 149 / 185 (81.08%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 150 / 185 (81.62%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 151 / 185 (82.16%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 152 / 185 (82.70%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 153 / 185 (83.24%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 154 / 185 (83.78%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 155 / 185 (84.32%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 156 / 185 (84.86%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 157 / 185 (85.41%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 158 / 185 (85.95%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 159 / 185 (86.49%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 160 / 185 (87.03%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 161 / 185 (87.57%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 162 / 185 (88.11%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 163 / 185 (88.65%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 164 / 185 (89.19%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 165 / 185 (89.73%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 166 / 185 (90.27%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 167 / 185 (90.81%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 168 / 185 (91.35%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 169 / 185 (91.89%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 170 / 185 (92.43%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 171 / 185 (92.97%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 172 / 185 (93.51%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 173 / 185 (94.05%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 174 / 185 (94.59%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 175 / 185 (95.14%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 176 / 185 (95.68%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 177 / 185 (96.22%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 178 / 185 (96.76%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 179 / 185 (97.30%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 180 / 185 (97.84%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 181 / 185 (98.38%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 182 / 185 (98.92%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 183 / 185 (99.46%), skipped 0 / 185 (0.00%)
[19:24:50 AlignOverlaps] Aligning overlap: 184 / 185 (100.00%), skipped 0 / 185 (0.00%)

[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 0 bp to 499 bp (0.00%), coverage: 25x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 500 bp to 999 bp (1.06%), coverage: 25x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 1000 bp to 1499 bp (2.12%), coverage: 28x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 1500 bp to 1999 bp (3.18%), coverage: 26x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 2000 bp to 2499 bp (4.24%), coverage: 27x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 2500 bp to 2999 bp (5.30%), coverage: 24x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 3000 bp to 3499 bp (6.36%), coverage: 30x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 3500 bp to 3999 bp (7.42%), coverage: 21x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 4000 bp to 4499 bp (8.48%), coverage: 22x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 4500 bp to 4999 bp (9.54%), coverage: 19x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 5000 bp to 5499 bp (10.60%), coverage: 25x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 5500 bp to 5999 bp (11.66%), coverage: 21x
[19:24:50 CreateConsensusAln] (thread_id = 0) Processing window: 6000 bp to 6499 bp (12.72%), coverage: 25x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 6500 bp to 6999 bp (13.78%), coverage: 23x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 7000 bp to 7499 bp (14.84%), coverage: 28x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 7500 bp to 7999 bp (15.90%), coverage: 26x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 8000 bp to 8499 bp (16.96%), coverage: 27x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 8500 bp to 8999 bp (18.02%), coverage: 24x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 9000 bp to 9499 bp (19.08%), coverage: 21x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 9500 bp to 9999 bp (20.14%), coverage: 25x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 10000 bp to 10499 bp (21.20%), coverage: 25x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 10500 bp to 10999 bp (22.26%), coverage: 20x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 11000 bp to 11499 bp (23.32%), coverage: 21x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 11500 bp to 11999 bp (24.38%), coverage: 22x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 12000 bp to 12499 bp (25.44%), coverage: 21x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 12500 bp to 12999 bp (26.50%), coverage: 21x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 13000 bp to 13499 bp (27.57%), coverage: 23x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 13500 bp to 13999 bp (28.63%), coverage: 22x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 14000 bp to 14499 bp (29.69%), coverage: 24x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 14500 bp to 14999 bp (30.75%), coverage: 27x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 15000 bp to 15499 bp (31.81%), coverage: 24x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 15500 bp to 15999 bp (32.87%), coverage: 22x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 16000 bp to 16499 bp (33.93%), coverage: 24x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 16500 bp to 16999 bp (34.99%), coverage: 25x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 17000 bp to 17499 bp (36.05%), coverage: 28x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 17500 bp to 17999 bp (37.11%), coverage: 30x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 18000 bp to 18499 bp (38.17%), coverage: 32x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 18500 bp to 18999 bp (39.23%), coverage: 23x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 19000 bp to 19499 bp (40.29%), coverage: 30x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 19500 bp to 19999 bp (41.35%), coverage: 34x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 20000 bp to 20499 bp (42.41%), coverage: 35x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 20500 bp to 20999 bp (43.47%), coverage: 31x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 21000 bp to 21499 bp (44.53%), coverage: 30x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 21500 bp to 21999 bp (45.59%), coverage: 32x
[19:24:51 CreateConsensusAln] (thread_id = 0) Processing window: 22000 bp to 22499 bp (46.65%), coverage: 38x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 22500 bp to 22999 bp (47.71%), coverage: 32x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 23000 bp to 23499 bp (48.77%), coverage: 28x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 23500 bp to 23999 bp (49.83%), coverage: 25x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 24000 bp to 24499 bp (50.89%), coverage: 27x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 24500 bp to 24999 bp (51.95%), coverage: 31x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 25000 bp to 25499 bp (53.01%), coverage: 29x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 25500 bp to 25999 bp (54.07%), coverage: 30x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 26000 bp to 26499 bp (55.13%), coverage: 27x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 26500 bp to 26999 bp (56.19%), coverage: 28x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 27000 bp to 27499 bp (57.25%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 27500 bp to 27999 bp (58.31%), coverage: 23x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 28000 bp to 28499 bp (59.37%), coverage: 24x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 28500 bp to 28999 bp (60.43%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 29000 bp to 29499 bp (61.49%), coverage: 21x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 29500 bp to 29999 bp (62.55%), coverage: 19x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 30000 bp to 30499 bp (63.61%), coverage: 16x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 30500 bp to 30999 bp (64.67%), coverage: 15x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 31000 bp to 31499 bp (65.73%), coverage: 17x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 31500 bp to 31999 bp (66.79%), coverage: 16x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 32000 bp to 32499 bp (67.85%), coverage: 14x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 32500 bp to 32999 bp (68.91%), coverage: 17x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 33000 bp to 33499 bp (69.97%), coverage: 11x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 33500 bp to 33999 bp (71.03%), coverage: 14x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 34000 bp to 34499 bp (72.09%), coverage: 14x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 34500 bp to 34999 bp (73.15%), coverage: 10x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 35000 bp to 35499 bp (74.21%), coverage: 13x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 35500 bp to 35999 bp (75.27%), coverage: 11x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 36000 bp to 36499 bp (76.33%), coverage: 14x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 36500 bp to 36999 bp (77.39%), coverage: 11x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 37000 bp to 37499 bp (78.45%), coverage: 15x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 37500 bp to 37999 bp (79.51%), coverage: 13x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 38000 bp to 38499 bp (80.58%), coverage: 11x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 38500 bp to 38999 bp (81.64%), coverage: 11x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 39000 bp to 39499 bp (82.70%), coverage: 17x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 39500 bp to 39999 bp (83.76%), coverage: 16x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 40000 bp to 40499 bp (84.82%), coverage: 20x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 40500 bp to 40999 bp (85.88%), coverage: 19x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 41000 bp to 41499 bp (86.94%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 41500 bp to 41999 bp (88.00%), coverage: 23x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 42000 bp to 42499 bp (89.06%), coverage: 24x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 42500 bp to 42999 bp (90.12%), coverage: 23x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 43000 bp to 43499 bp (91.18%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 43500 bp to 43999 bp (92.24%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 44000 bp to 44499 bp (93.30%), coverage: 22x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 44500 bp to 44999 bp (94.36%), coverage: 23x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 45000 bp to 45499 bp (95.42%), coverage: 24x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 45500 bp to 45999 bp (96.48%), coverage: 21x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 46000 bp to 46499 bp (97.54%), coverage: 23x
[19:24:52 CreateConsensusAln] (thread_id = 0) Processing window: 46500 bp to 46999 bp (98.60%), coverage: 22x
[19:24:53 CreateConsensusAln] (thread_id = 0) Processing window: 47000 bp to 47499 bp (99.66%), coverage: 14x[19:24:53 CreateConsensusAln] Batch checkpoint: Performed consensus on all windows, joining the windows now.
[19:24:53 CreateConsensusAln] Batch checkpoint: Processed 20000 windows and exported the consensus.[19:24:53 ConsensusFromOverlaps] Processed 47161 bp of 47161 bp (100.00%)

Racon exited.
rm: cannot remove ‘results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.report’: No such file or directory
Building alignments
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref" of length 48503
# construct suffix tree for sequence of length 48503
# (maximum reference length is 536870908)
# (maximum query length is<PHONE_NUMBER>)
# CONSTRUCTIONTIME /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.01
# reading input file "/lustre/work-lustre/waterhouse_team/apps/racon/results/consensus-lambda_30x_ont-paf-align-iter1.fasta" of length 47917
# matching query-file "/lustre/work-lustre/waterhouse_team/apps/racon/results/consensus-lambda_30x_ont-paf-align-iter1.fasta"
# against subject-file "results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref"
# COMPLETETIME /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.02
# SPACE /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.09
4: FINISHING DATA
Filtering alignments
Extracting alignment coordinates
Analyzing SNPs
Extracting alignment breakpoints
Generating report file
TotalBases                     48502                47917
AlignedBases           48438(99.87%)       47917(100.00%)
AvgIdentity                    97.58                97.58
AvgIdentity                    97.58                97.58
Command line: tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter0.fasta test-data/lambda/reads.fastq.fasta
Real time: 0.24 s
CPU time: -1.0 s
User time: 0.05 s
System time: 0.00 s
Maximum RSS: 5284 kB
Exit status: 0
Command line: bin/racon -M 5 -X -4 -G -8 -E -6 --bq 10 -t 1 test-data/lambda/reads.fastq results/temp/consensus-lambda_30x_ont-paf-align-iter1.paf results/consensus-lambda_30x_ont-paf-align-iter0.fasta results/consensus-lambda_30x_ont-paf-align-iter1.fasta
Real time: 3.61 s
CPU time: -1.0 s
User time: 3.55 s
System time: 0.02 s
Maximum RSS: 31168 kB
Exit status: 0

Evaluating the results.

Running MUMmer on contig: "Consensus_utg000001l"
Executing command: "nucmer --maxmatch --extend -p results/temp-ed/nucmer test-data/lambda/NC_001416.fa results/temp-ed/singlecontig.fasta; delta-filter -r -q results/temp-ed/nucmer.delta > results/temp-ed/nucmer.filt.delta; show-coords -r -c results/temp-ed/nucmer.filt.delta > results/temp-ed/nucmer.filt.coords"

Parsing the coords file.
state_coord_lines =  True
33    48470  |        1    47917  |    48438    47917  |    97.58  |    99.87   100.00  | NC_001416	Consensus_utg000001l
['33', '48470', '|', '1', '47917', '|', '48438', '47917', '|', '97.58', '|', '99.87', '100.00', '|', 'NC_001416', 'Consensus_utg000001l']
fwd =  True
correct_orient =  True
Printing frags:
[33, 48470, 1, 47917, True, 'NC_001416', 'Consensus_utg000001l']

coords: "[33, 48470, 1, 47917, True, 'NC_001416', 'Consensus_utg000001l']"
lines:
/lustre/work-lustre/waterhouse_team/apps/racon/test-data/lambda/NC_001416.fa /lustre/work-lustre/waterhouse_team/apps/racon/results/temp-ed/singlecontig.fasta

NUCMER

    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [COV R]  [COV Q]  | [TAGS]

==========================================================================================================

      33    48470  |        1    47917  |    48438    47917  |    97.58  |    99.87   100.00  | NC_001416	Consensus_utg000001l

Running Edlib to determine the edit distance...
Executing command: "/lustre/work-lustre/waterhouse_team/apps/racon/scripts/../tools/edlib/src/aligner results/temp-ed/nw-contig.0.fasta results/temp-ed/nw-ref.0.fasta -m NW"

Final edit distance: 1240, aligned edit distance: 1176, unaligned ref len: 64, aligned ref len: 48438, aligned contig len: 47917

{'NC_001416': 0}

tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter1.fasta test-data/lambda/reads.fastq.fasta > results/temp/consensus-lambda_30x_ont-paf-align-iter2.paf
[M::mm_idx_gen::0.002*0.00] collected minimizers
[M::mm_idx_gen::0.005*0.87] sorted minimizers
[M::main::0.005*0.87] loaded/built the index for 1 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 2
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter1.fasta test-data/lambda/reads.fastq.fasta
[M::main] Real time: 0.036 sec; CPU: 0.064 sec
test-data/lambda/reads.fastq

Running Racon:
    bin/racon -M 5 -X -4 -G -8 -E -6 --bq 10 -t 1 test-data/lambda/reads.fastq results/temp/consensus-lambda_30x_ont-paf-align-iter2.paf results/consensus-lambda_30x_ont-paf-align-iter1.fasta results/consensus-lambda_30x_ont-paf-align-iter2.fasta
[19:24:55 main] Using PAF for input alignments. (results/temp/consensus-lambda_30x_ont-paf-align-iter2.paf)
[19:24:55 main] Loading reads.
[19:24:55 main] Hashing qnames.
[19:24:55 main] Parsing the overlaps file.
[19:24:55 main] Unique overlaps will be filtered on the fly.
[19:24:55 main] Overlaps will be fully aligned.
[19:24:55 ConsensusFromOverlaps] Running consensus.
[19:24:55 ConsensusFromOverlaps] Separating overlaps to individual contigs.
[19:24:55 ConsensusFromOverlaps] In total, there are 1 contigs for consensus, each containing:
[19:24:55 ConsensusFromOverlaps] 	[0] Consensus_utg000001l 198 alignments, contig len: 47917

[19:24:55 ConsensusFromOverlaps] Started processing contig 1 / 1 (100.00%): Consensus_utg000001l
[19:24:55 ConsensusFromOverlaps] (thread_id = 0) Aligning overlaps for contig 1 / 1 (100.00%): Consensus_utg000001l

[19:24:55 AlignOverlaps] Aligning overlap: 0 / 197 (0.51%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 1 / 197 (1.02%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 2 / 197 (1.52%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 3 / 197 (2.03%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 4 / 197 (2.54%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 5 / 197 (3.05%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 6 / 197 (3.55%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 7 / 197 (4.06%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 8 / 197 (4.57%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 9 / 197 (5.08%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 10 / 197 (5.58%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 11 / 197 (6.09%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 12 / 197 (6.60%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 13 / 197 (7.11%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 14 / 197 (7.61%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 15 / 197 (8.12%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 16 / 197 (8.63%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 17 / 197 (9.14%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 18 / 197 (9.64%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 19 / 197 (10.15%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 20 / 197 (10.66%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 21 / 197 (11.17%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 22 / 197 (11.68%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 23 / 197 (12.18%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 24 / 197 (12.69%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 25 / 197 (13.20%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 26 / 197 (13.71%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 27 / 197 (14.21%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 28 / 197 (14.72%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 29 / 197 (15.23%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 30 / 197 (15.74%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 31 / 197 (16.24%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 32 / 197 (16.75%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 33 / 197 (17.26%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 34 / 197 (17.77%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 35 / 197 (18.27%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 36 / 197 (18.78%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 37 / 197 (19.29%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 38 / 197 (19.80%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 39 / 197 (20.30%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 40 / 197 (20.81%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 41 / 197 (21.32%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 42 / 197 (21.83%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 43 / 197 (22.34%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 44 / 197 (22.84%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 45 / 197 (23.35%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 46 / 197 (23.86%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 47 / 197 (24.37%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 48 / 197 (24.87%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 49 / 197 (25.38%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 50 / 197 (25.89%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 51 / 197 (26.40%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 52 / 197 (26.90%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 53 / 197 (27.41%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 54 / 197 (27.92%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 55 / 197 (28.43%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 56 / 197 (28.93%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 57 / 197 (29.44%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 58 / 197 (29.95%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 59 / 197 (30.46%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 60 / 197 (30.96%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 61 / 197 (31.47%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 62 / 197 (31.98%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 63 / 197 (32.49%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 64 / 197 (32.99%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 65 / 197 (33.50%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 66 / 197 (34.01%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 67 / 197 (34.52%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 68 / 197 (35.03%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 69 / 197 (35.53%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 70 / 197 (36.04%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 71 / 197 (36.55%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 72 / 197 (37.06%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 73 / 197 (37.56%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 74 / 197 (38.07%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 75 / 197 (38.58%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 76 / 197 (39.09%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 77 / 197 (39.59%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 78 / 197 (40.10%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 79 / 197 (40.61%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 80 / 197 (41.12%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 81 / 197 (41.62%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 82 / 197 (42.13%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 83 / 197 (42.64%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 84 / 197 (43.15%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 85 / 197 (43.65%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 86 / 197 (44.16%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 87 / 197 (44.67%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 88 / 197 (45.18%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 89 / 197 (45.69%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 90 / 197 (46.19%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 91 / 197 (46.70%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 92 / 197 (47.21%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 93 / 197 (47.72%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 94 / 197 (48.22%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 95 / 197 (48.73%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 96 / 197 (49.24%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 97 / 197 (49.75%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 98 / 197 (50.25%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 99 / 197 (50.76%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 100 / 197 (51.27%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 101 / 197 (51.78%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 102 / 197 (52.28%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 103 / 197 (52.79%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 104 / 197 (53.30%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 105 / 197 (53.81%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 106 / 197 (54.31%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 107 / 197 (54.82%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 108 / 197 (55.33%), skipped 0 / 197 (0.00%)
[19:24:55 AlignOverlaps] Aligning overlap: 109 / 197 (55.84%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 110 / 197 (56.35%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 111 / 197 (56.85%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 112 / 197 (57.36%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 113 / 197 (57.87%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 114 / 197 (58.38%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 115 / 197 (58.88%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 116 / 197 (59.39%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 117 / 197 (59.90%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 118 / 197 (60.41%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 119 / 197 (60.91%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 120 / 197 (61.42%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 121 / 197 (61.93%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 122 / 197 (62.44%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 123 / 197 (62.94%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 124 / 197 (63.45%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 125 / 197 (63.96%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 126 / 197 (64.47%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 127 / 197 (64.97%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 128 / 197 (65.48%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 129 / 197 (65.99%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 130 / 197 (66.50%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 131 / 197 (67.01%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 132 / 197 (67.51%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 133 / 197 (68.02%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 134 / 197 (68.53%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 135 / 197 (69.04%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 136 / 197 (69.54%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 137 / 197 (70.05%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 138 / 197 (70.56%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 139 / 197 (71.07%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 140 / 197 (71.57%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 141 / 197 (72.08%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 142 / 197 (72.59%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 143 / 197 (73.10%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 144 / 197 (73.60%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 145 / 197 (74.11%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 146 / 197 (74.62%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 147 / 197 (75.13%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 148 / 197 (75.63%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 149 / 197 (76.14%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 150 / 197 (76.65%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 151 / 197 (77.16%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 152 / 197 (77.66%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 153 / 197 (78.17%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 154 / 197 (78.68%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 155 / 197 (79.19%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 156 / 197 (79.70%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 157 / 197 (80.20%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 158 / 197 (80.71%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 159 / 197 (81.22%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 160 / 197 (81.73%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 161 / 197 (82.23%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 162 / 197 (82.74%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 163 / 197 (83.25%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 164 / 197 (83.76%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 165 / 197 (84.26%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 166 / 197 (84.77%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 167 / 197 (85.28%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 168 / 197 (85.79%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 169 / 197 (86.29%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 170 / 197 (86.80%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 171 / 197 (87.31%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 172 / 197 (87.82%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 173 / 197 (88.32%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 174 / 197 (88.83%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 175 / 197 (89.34%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 176 / 197 (89.85%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 177 / 197 (90.36%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 178 / 197 (90.86%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 179 / 197 (91.37%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 180 / 197 (91.88%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 181 / 197 (92.39%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 182 / 197 (92.89%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 183 / 197 (93.40%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 184 / 197 (93.91%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 185 / 197 (94.42%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 186 / 197 (94.92%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 187 / 197 (95.43%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 188 / 197 (95.94%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 189 / 197 (96.45%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 190 / 197 (96.95%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 191 / 197 (97.46%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 192 / 197 (97.97%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 193 / 197 (98.48%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 194 / 197 (98.98%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 195 / 197 (99.49%), skipped 0 / 197 (0.00%)
[19:24:56 AlignOverlaps] Aligning overlap: 196 / 197 (100.00%), skipped 0 / 197 (0.00%)

[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 0 bp to 499 bp (0.00%), coverage: 27x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 500 bp to 999 bp (1.04%), coverage: 25x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 1000 bp to 1499 bp (2.09%), coverage: 29x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 1500 bp to 1999 bp (3.13%), coverage: 25x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 2000 bp to 2499 bp (4.17%), coverage: 27x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 2500 bp to 2999 bp (5.22%), coverage: 24x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 3000 bp to 3499 bp (6.26%), coverage: 30x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 3500 bp to 3999 bp (7.30%), coverage: 23x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 4000 bp to 4499 bp (8.35%), coverage: 25x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 4500 bp to 4999 bp (9.39%), coverage: 20x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 5000 bp to 5499 bp (10.43%), coverage: 24x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 5500 bp to 5999 bp (11.48%), coverage: 24x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 6000 bp to 6499 bp (12.52%), coverage: 27x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 6500 bp to 6999 bp (13.57%), coverage: 22x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 7000 bp to 7499 bp (14.61%), coverage: 27x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 7500 bp to 7999 bp (15.65%), coverage: 25x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 8000 bp to 8499 bp (16.70%), coverage: 34x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 8500 bp to 8999 bp (17.74%), coverage: 24x
[19:24:56 CreateConsensusAln] (thread_id = 0) Processing window: 9000 bp to 9499 bp (18.78%), coverage: 23x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 9500 bp to 9999 bp (19.83%), coverage: 29x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 10000 bp to 10499 bp (20.87%), coverage: 24x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 10500 bp to 10999 bp (21.91%), coverage: 21x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 11000 bp to 11499 bp (22.96%), coverage: 21x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 11500 bp to 11999 bp (24.00%), coverage: 23x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 12000 bp to 12499 bp (25.04%), coverage: 19x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 12500 bp to 12999 bp (26.09%), coverage: 21x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 13000 bp to 13499 bp (27.13%), coverage: 23x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 13500 bp to 13999 bp (28.17%), coverage: 26x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 14000 bp to 14499 bp (29.22%), coverage: 26x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 14500 bp to 14999 bp (30.26%), coverage: 30x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 15000 bp to 15499 bp (31.30%), coverage: 28x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 15500 bp to 15999 bp (32.35%), coverage: 28x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 16000 bp to 16499 bp (33.39%), coverage: 24x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 16500 bp to 16999 bp (34.43%), coverage: 27x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 17000 bp to 17499 bp (35.48%), coverage: 28x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 17500 bp to 17999 bp (36.52%), coverage: 30x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 18000 bp to 18499 bp (37.56%), coverage: 32x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 18500 bp to 18999 bp (38.61%), coverage: 36x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 19000 bp to 19499 bp (39.65%), coverage: 26x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 19500 bp to 19999 bp (40.70%), coverage: 31x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 20000 bp to 20499 bp (41.74%), coverage: 35x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 20500 bp to 20999 bp (42.78%), coverage: 37x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 21000 bp to 21499 bp (43.83%), coverage: 35x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 21500 bp to 21999 bp (44.87%), coverage: 36x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 22000 bp to 22499 bp (45.91%), coverage: 41x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 22500 bp to 22999 bp (46.96%), coverage: 39x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 23000 bp to 23499 bp (48.00%), coverage: 35x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 23500 bp to 23999 bp (49.04%), coverage: 31x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 24000 bp to 24499 bp (50.09%), coverage: 26x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 24500 bp to 24999 bp (51.13%), coverage: 28x
[19:24:57 CreateConsensusAln] (thread_id = 0) Processing window: 25000 bp to 25499 bp (52.17%), coverage: 32x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 25500 bp to 25999 bp (53.22%), coverage: 30x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 26000 bp to 26499 bp (54.26%), coverage: 29x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 26500 bp to 26999 bp (55.30%), coverage: 28x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 27000 bp to 27499 bp (56.35%), coverage: 27x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 27500 bp to 27999 bp (57.39%), coverage: 26x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 28000 bp to 28499 bp (58.43%), coverage: 21x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 28500 bp to 28999 bp (59.48%), coverage: 19x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 29000 bp to 29499 bp (60.52%), coverage: 23x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 29500 bp to 29999 bp (61.56%), coverage: 20x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 30000 bp to 30499 bp (62.61%), coverage: 21x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 30500 bp to 30999 bp (63.65%), coverage: 17x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 31000 bp to 31499 bp (64.70%), coverage: 16x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 31500 bp to 31999 bp (65.74%), coverage: 16x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 32000 bp to 32499 bp (66.78%), coverage: 16x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 32500 bp to 32999 bp (67.83%), coverage: 16x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 33000 bp to 33499 bp (68.87%), coverage: 15x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 33500 bp to 33999 bp (69.91%), coverage: 16x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 34000 bp to 34499 bp (70.96%), coverage: 14x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 34500 bp to 34999 bp (72.00%), coverage: 14x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 35000 bp to 35499 bp (73.04%), coverage: 14x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 35500 bp to 35999 bp (74.09%), coverage: 11x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 36000 bp to 36499 bp (75.13%), coverage: 12x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 36500 bp to 36999 bp (76.17%), coverage: 12x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 37000 bp to 37499 bp (77.22%), coverage: 14x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 37500 bp to 37999 bp (78.26%), coverage: 11x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 38000 bp to 38499 bp (79.30%), coverage: 15x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 38500 bp to 38999 bp (80.35%), coverage: 14x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 39000 bp to 39499 bp (81.39%), coverage: 11x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 39500 bp to 39999 bp (82.43%), coverage: 12x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 40000 bp to 40499 bp (83.48%), coverage: 17x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 40500 bp to 40999 bp (84.52%), coverage: 17x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 41000 bp to 41499 bp (85.56%), coverage: 18x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 41500 bp to 41999 bp (86.61%), coverage: 22x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 42000 bp to 42499 bp (87.65%), coverage: 21x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 42500 bp to 42999 bp (88.70%), coverage: 24x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 43000 bp to 43499 bp (89.74%), coverage: 23x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 43500 bp to 43999 bp (90.78%), coverage: 24x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 44000 bp to 44499 bp (91.83%), coverage: 22x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 44500 bp to 44999 bp (92.87%), coverage: 22x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 45000 bp to 45499 bp (93.91%), coverage: 23x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 45500 bp to 45999 bp (94.96%), coverage: 22x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 46000 bp to 46499 bp (96.00%), coverage: 24x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 46500 bp to 46999 bp (97.04%), coverage: 24x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 47000 bp to 47499 bp (98.09%), coverage: 23x
[19:24:58 CreateConsensusAln] (thread_id = 0) Processing window: 47500 bp to 47999 bp (99.13%), coverage: 20x[19:24:58 CreateConsensusAln] Batch checkpoint: Performed consensus on all windows, joining the windows now.
[19:24:58 CreateConsensusAln] Batch checkpoint: Processed 20000 windows and exported the consensus.[19:24:58 ConsensusFromOverlaps] Processed 47917 bp of 47917 bp (100.00%)

Racon exited.
Building alignments
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref" of length 48503
# construct suffix tree for sequence of length 48503
# (maximum reference length is 536870908)
# (maximum query length is<PHONE_NUMBER>)
# CONSTRUCTIONTIME /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.01
# reading input file "/lustre/work-lustre/waterhouse_team/apps/racon/results/consensus-lambda_30x_ont-paf-align-iter2.fasta" of length 47873
# matching query-file "/lustre/work-lustre/waterhouse_team/apps/racon/results/consensus-lambda_30x_ont-paf-align-iter2.fasta"
# against subject-file "results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref"
# COMPLETETIME /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.02
# SPACE /work/waterhouse_team/miniconda2/opt/mummer-3.23/mummer results/temp/dnadiff-lambda_30x_ont/racon-lambda_30x_ont-paf-align.ntref 0.09
4: FINISHING DATA
Filtering alignments
Extracting alignment coordinates
Analyzing SNPs
Extracting alignment breakpoints
Generating report file
TotalBases                     48502                47873
AlignedBases           48434(99.86%)       47873(100.00%)
AvgIdentity                    97.96                97.96
AvgIdentity                    97.96                97.96
Command line: tools/minimap/minimap results/consensus-lambda_30x_ont-paf-align-iter1.fasta test-data/lambda/reads.fastq.fasta
Real time: 0.03 s
CPU time: -1.0 s
User time: 0.06 s
System time: 0.00 s
Maximum RSS: 5260 kB
Exit status: 0
Command line: bin/racon -M 5 -X -4 -G -8 -E -6 --bq 10 -t 1 test-data/lambda/reads.fastq results/temp/consensus-lambda_30x_ont-paf-align-iter2.paf results/consensus-lambda_30x_ont-paf-align-iter1.fasta results/consensus-lambda_30x_ont-paf-align-iter2.fasta
Real time: 3.38 s
CPU time: -1.0 s
User time: 3.35 s
System time: 0.03 s
Maximum RSS: 26268 kB
Exit status: 0

Evaluating the results.

Running MUMmer on contig: "Consensus_Consensus_utg000001l"
Executing command: "nucmer --maxmatch --extend -p results/temp-ed/nucmer test-data/lambda/NC_001416.fa results/temp-ed/singlecontig.fasta; delta-filter -r -q results/temp-ed/nucmer.delta > results/temp-ed/nucmer.filt.delta; show-coords -r -c results/temp-ed/nucmer.filt.delta > results/temp-ed/nucmer.filt.coords"

Parsing the coords file.
state_coord_lines =  True
36    48469  |        1    47873  |    48434    47873  |    97.96  |    99.86   100.00  | NC_001416	Consensus_Consensus_utg000001l
['36', '48469', '|', '1', '47873', '|', '48434', '47873', '|', '97.96', '|', '99.86', '100.00', '|', 'NC_001416', 'Consensus_Consensus_utg000001l']
fwd =  True
correct_orient =  True
Printing frags:
[36, 48469, 1, 47873, True, 'NC_001416', 'Consensus_Consensus_utg000001l']

coords: "[36, 48469, 1, 47873, True, 'NC_001416', 'Consensus_Consensus_utg000001l']"
lines:
/lustre/work-lustre/waterhouse_team/apps/racon/test-data/lambda/NC_001416.fa /lustre/work-lustre/waterhouse_team/apps/racon/results/temp-ed/singlecontig.fasta

NUCMER

    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [COV R]  [COV Q]  | [TAGS]

==========================================================================================================

      36    48469  |        1    47873  |    48434    47873  |    97.96  |    99.86   100.00  | NC_001416	Consensus_Consensus_utg000001l

Running Edlib to determine the edit distance...
Executing command: "/lustre/work-lustre/waterhouse_team/apps/racon/scripts/../tools/edlib/src/aligner results/temp-ed/nw-contig.0.fasta results/temp-ed/nw-ref.0.fasta -m NW"

Final edit distance: 1057, aligned edit distance: 989, unaligned ref len: 68, aligned ref len: 48434, aligned contig len: 47873

{'NC_001416': 0}

-----
PBS Job 1786423.pbs
CPU time  : 00:00:10
Wall time : 00:00:22
Mem usage : 28264kb

The output looks fine (you can remove it as it is quite large and makes scrolling troublesome :D). Could you please send me the file sizes of 'Fruit.gfa.fasta' and 'Fruit.gfa1.paf'? Also, try running racon from its root folder on the fruit dataset to see if it will throw illegal instruction again.
Best regards,
Robert

Hi, This are the filesizes:

Fruit.gfa1.paf (150G)
Fruit.gfa.fasta (1.2G)

I have just started to run it from the root folder.

p.s. I created a fruit folder inside racon directory next bin, src and tools... Next, I copied all files from the previous run to fruit folder. I executed the commands from the same position as 'example1_1-paf-lambda-align.sh'.
Unfortunately, I still got:
[M::mm_idx_gen::34.759*1.55] collected minimizers
[M::mm_idx_gen::41.500*1.77] sorted minimizers
[M::main::41.500*1.77] loaded/built the index for 250197 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 114
[M::main] Version: 0.2-r123
[M::main] CMD: minimap Fruit/Fruit.gfa.fasta /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq
[M::main] Real time: 7083.955 sec; CPU: 23207.744 sec
/var/spool/PBS/mom_priv/jobs/1807252.pbs.SC: line 40: 41259 Illegal instruction     racon -t 18 /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq Fruit/Fruit.gfa1.paf Fruit/Fruit.gfa.fasta Fruit/Fruit.racon1.fasta
/var/spool/PBS/mom_priv/jobs/1807252.pbs.SC: line 46: 41260 Segmentation fault      minimap Fruit/Fruit.racon1.fasta /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq > Fruit/Fruit.gfa2.paf
/var/spool/PBS/mom_priv/jobs/1807252.pbs.SC: line 53: 41261 Illegal instruction     racon -t 18 /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq Fruit/Fruit.gfa2.paf Fruit/Fruit.racon1.fasta Fruit/Fruit.racon2.fasta

Did I miss understand you?

Try running './bin/racon -t 18 /work/lorencm/All_RawData/RSnSeQ_110Fruit.fastq Fruit/Fruit.gfa1.paf Fruit/Fruit.gfa.fasta Fruit/Fruit.racon1.fasta'.

./bin/racon -t 18 ...worked rather racon -t 18 .... Would it be possible to fix it that racon -t 18 ... would work, too?
The above awk command to convert gfa to fasta file was wrong, too. It should be awk '/^S/{print ">"$2; print $3}' Fruit | fold  Fruit.gfa.fasta.

Check if racon executable is in /usr/bin. If yes, remove it and add the racon directory to .bashrc, if you haven't yet. To check if it works now, run racon ("racon -t 18 ....") with simple data, i.e. lambda from test folder.


Fix html typo in auth example

The html was probably copy pasted from the CSRF example but the auth example has nothing to do with CSRF so I adjusted the html titles accordingly.

Thanks! 😂


feat(NX-3082): Change artwork and CTAs copies

The type of this PR is: Feature

This PR resolves NX-3082
Description
We're changing the copies around Buy now, Make offer and Contact for Price but only the copies, we are not touching in any saleMessage coming from Gravity or other services, nor the language elsewhere, example we still call Buy now everything related to it, only the copy has changed to Purchase.
Price on Request

Purchase and Make an Offer

Make an Offer

PR Checklist (tick all before merging)

[x] I have included screenshots or videos to illustrate my changes, or I have not changed anything that impacts the UI.
[x] I have tested my changes on iOS and Android.
[x] I have added tests/stories for my changes, or my changes don't require testing/stories, or I have included a link to a separate Jira ticket covering the tests.
[x] I have added a feature flag, or my changes don't require a feature flag. (How do I add one?)
[x] I have documented any follow-up work that this PR will require, or it does not require any.
[x] I have added an app state migration, or my changes do not require one. (What are migrations?)
[x] I have added a changelog entry below or my changes do not require one.

To the reviewers 👀

[ ] I would like at least one of the reviewers to run this PR on the simulator or device.

Changelog updates
Changelog updates

Cross-platform user-facing changes

change copies Buy Now, Make Offer and Contact For Price - araujobarret

iOS user-facing changes

Android user-facing changes

Dev changes

This PR contains the following changes:

Cross-platform user-facing changes (change copies Buy Now, Make Offer and Contact For Price - araujobarret)

  Generated by :no_entry_sign: dangerJS against d56578b9420d148c851cada3de16a22bd6dce8d1

nice!
i find "Price on Request" weird sounding and harder to understand than "Contact for price", but im not a native speaker so it might be that.

I did not take part into that, Product conducted the research and decided on that, I trust them 😃

also, are we changing the BNMO shortening to PMO? 😛

Well, we're not there yet, all models and references we have in Designs, Product documentation, and code would need to be changed, for now we keep the idea of BNMO 😂


Support for ANSI TTY Esc Colorization Codes

Do you think it is reasonable/feasible to have it auto-detect ANSI TTY color codes and both hide the ANSI TTY codes and use them to colorize the text.
That would be awesome for simply streaming stderr output and other similarly embedded pre-colorized streams of data.
I'm interested in doing the work, but would like to know if the author thinks it is feasible.
See also this tool
And related comments
Visual Studio Marketplace comments

The output detection works differently than you might think. For instance, one can't actually set the output color of a line. One can only classify a line as a particular type that is associated with a color. The classification is sometimes ignored when there are conflicting circumstances. The other thing VS does not allow is changing the actual text of the output window. For instance, I've had several requests to suppress lines of output in the debug view. Can't do it because VS does not provide a hook to modify text.
So while a good idea, there would be no way to remove the escacpe sequences from the output. The sections could be colored but the escape codes would remain.

I wonder if simply making another VS (channel) log-panel-window might be
an easier more flexible solution then?
Thoughts...?
p.s., I can't remember at the moment what VS actually calls the set of
panels that are grouped with build, etc. But I remember they are not too
hard to create; it's been quite a while since I was on the Microsoft
DevDiv Team working on VS.

Mike Ward<EMAIL_ADDRESS>Saturday, July 14, 2018 8:00 AM
The output detection works differently than you might think. For
instance, one can't actually set the output color of a line. One can
only classify a line as a particular type that is associated with a
color. The classification is sometimes ignored when there are
conflicting circumstances. The other thing VS does not allow is
changing the actual text of the output window. For instance, I've had
several requests to suppress lines of output in the debug view. Can't
do it because VS does not provide a hook to modify text.
So while a good idea, there would be no way to remove the escacpe
sequences from the output. The sections could be colored but the
escape codes would remain.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/mike-ward/VSColorOutput/issues/76#issuecomment-405028823,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AKB-n-NELNx291-myHjY9Ow1F2d1anZNks5uGgefgaJpZM4VPtfj.

This is an old issue but still valid.
In my case webpack produces a lot of colored console text like this:
1>assets by chunk 8.95 MiB (name: main)
1>  asset bundle.js 7.91 MiB [emitted] (name: main)
1>  asset bundle.css 1.03 MiB [emitted] (name: main)
1>assets by info 530 KiB [immutable]

When I run the command in a terminal (inside Visual Studio) the colors look fine!
When running as part of the build, the output window only shows the above uncolored message

@Khaos66 As stated above, there is no hook to modify the output text in the build window. This is limitation that Visual Studio imposes.

When I run the command in a terminal (inside Visual Studio) the colors look fine!

The terminal window has a terminal shell, the build window does not.

Writing an ANSI tty escape filter to remove them is a small amount of code. And not too much more to convert them to make calls to some internal API.
With that said, plugging such a small library into context is the real work.

You could up-vote this
https://developercommunity.visualstudio.com/t/Support-or-skip-ASCI-TTY-formatings-in-t/10251549


consensus roothash events specialization

roothash events with related runtime and related runtime round

cutting this off here, moving messages to a new PR

the fact that there are no regression test breakages :skull:

the fact that there are no regression test breakages 💀

That's unexpected IMO. The PR modifies the ConsensusEvent openapi type, which is the return type of /consensus/events, which is in run.sh. Worth looking into more.

@mitjat ready for another review if you want to look

Error: cyclomatic complexity 31 of func convertEvent is high (> 30) (gocyclo)

oh my god

the pr:

+231 −17

the lint fix:

677 insertions(+), 610 deletions(-)

ok lots of unexplained cache changes, gotta figure this out

more discussion on the new field names: change them all to roothash_, no more related_. because there's no desire to generalize this to other event types

ok conclusions on other damask e2e cache changes:

emerald is currently disabled, and an empty cache has its hash seed reset each time. ignoring the diff
sourcify cache incorrectly ignored existing entries due to indexes being missing. I think I can resolve by regenerating the indexes
sourcify cache misc files missing is unintended. I'll regenerate and add
lock file added to sourcify cache is because we don't cleanly shut down the cache from the http proxy. ignoring the diff
event ordering is known not to have sufficient ORDER BY in api query. gonna push the diff and we can resolve separately

ok test caches should be set. next is the renames


Add response formation

Current coverage is 90.97% (diff: 91.48%)

No coverage report found for master at 552efd1.

Powered by Codecov. Last update 552efd1...5f62ee8


chore: replace dca-rs

Dca-rs does not exist anymore, replaced with the dca cli solution to create .dca

Sorry for such a long wait.

Dca-rs does not exist anymore
It actually does, however - here.
Though I think replacing it with solution from the dca itself would be a good idea.

Thanks for your contribution!


make reconnectionOwner object generic

https://github.com/microsoft/vscode/pull/155120#discussion_r920612599

fyi @Tyriar tracking this in an issue bc want to fix the bugs first and the PR I have out at the moment is already quite large

Np, good to push to August if needed.


Add ProxySettings for Nginx Reverse Proxy

Description of changes
Adds the recommendedProxySettings = true; option as it was needed for serving Hydra over to my own domain from localhost.
Things done

Built on platform(s)

[ ] x86_64-linux
[x] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[ ] Fits CONTRIBUTING.md.

Tested using these steps:
$ cd /path/to/nixpkgs/doc
$ nix-shell
[nix-shell]$ make

Hello, could you explain clearly the proposed change and why it is needed ? I don't see the link between pleroma and hydra.

No it's just with Hydra, it might be needed for that application and I am wrong. I'm mainly trying to make the option known that it is needed based on the service.

In NixOS most services do not handle the Nginx configuration and let the end user set up the reverse-proxy by themselves, potentially following the instructions from the upstream project.
You may want to add documentation in the NixOS wiki or the Hydra docs. I think the best course of action for this PR would be to close it.

That's fair! I'll look at Hydra.


Bump: 0.8.2-next -> 0.8.3

Proposed changes
This PR bumps NGSI Go version from Bump: 0.8.2-next -> 0.8.3.
Types of changes
What types of changes does your code introduce to the project: Put an x in the boxes that apply

[ ] Bugfix (non-breaking change which fixes an issue)
[X] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] Update only documentation, not any source code.

Checklist
Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of
them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before
merging your code.

[X] I have read the CONTRIBUTING doc
[ ] I have signed the CLA
[X] I have added tests that prove my fix is effective or that my feature works
[X] I have added necessary documentation (if appropriate)
[ ] Any dependent changes have been merged and published in downstream modules

Further comments
N/A

Coverage remained the same at 100.0% when pulling a7fa31305570ce27e1d5fc56c17efddb3f8e85e3 on fisuda:hardening/release_0.8.3 into 1c12b45267fb0499140dc7673086a8eff336be70 on lets-fiware:main.


Missed deviations for BGP route install OTG test

Copy changes from https://github.com/openconfig/featureprofiles/pull/871 to the OTG version of the test.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 55.741%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
1170

Relevant Lines:
2099

💛  - Coveralls