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[Bug]: QUAST for phased diploid assembly doesn't work #805

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ChiaraCampanelli opened this issue Nov 29, 2023 · 11 comments
Open

[Bug]: QUAST for phased diploid assembly doesn't work #805

ChiaraCampanelli opened this issue Nov 29, 2023 · 11 comments
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bug Something isn't working

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@ChiaraCampanelli
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What container were you trying to use, and how were you attempting to use it?

Is anybody know why the tool doesn't work when I give in input the diploid genome?
The diploid genome is generated by using HapDup starting from an assembly done by using long read sequencing data.

From the log file it seems that the analysis is completed but no file has been generated and the process keeps working forever.

Relevant log output

SLURM_JOB_PARTITION: batch
SLURM_NNODES: 1
SLURM_NODELIST: q28c27n3
SLURM_JOB_CPUS_PER_NODE: 36
Date: Thu Nov 23 15:55:38 CET 2023
Walltime: 03-00:00:00
========================================================================
INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
WARNING: While bind mounting '/scratch/leuven/357/vsc35717/tmp:/tmp': destination is already in the mount point list
/quast-5.2.0/quast.py hapdup_phased_1.fasta hapdup_phased_2.fasta --nanopore BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq -r /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -o quast_diploid --threads 36

Version: 5.2.0

System information:
  OS: Linux-4.18.0-425.13.1.el8_7.x86_64-x86_64-with-Ubuntu-20.04-focal (linux_64)
  Python version: 2.7.18
  CPUs number: 72

Started: 2023-11-23 15:55:41

CWD: /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf
Main parameters: 
  MODE: default, threads: 36, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Reference:
  /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna ==> GCA_000001405.15_GRCh38_no_alt_analysis_set

Contigs:
  Pre-processing...
  1  hapdup_phased_1.fasta ==> hapdup_phased_1
  2  hapdup_phased_2.fasta ==> hapdup_phased_2

2023-11-23 15:59:44
Running Reads analyzer...
  Logging to files /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.log and /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err...
  Will not search Structural Variations (needs paired-end reads)
  1  Pre-processing reads...
  1  Running BWA...
  2  Pre-processing reads...
  2  Running BWA...
  Pre-processing reads...
  Running BWA for reference...
  2  Done.
  2  Sorting SAM-file...
  2  Analysis is finished.
@ChiaraCampanelli ChiaraCampanelli added the bug Something isn't working label Nov 29, 2023
@kapsakcj
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It would help if you could tell us exactly which quast docker image was used as well as the command used to execute quast.

Additionally please share an error message (if it exists?). The log file you shared looks like there were only warnings, but no errors?

@ChiaraCampanelli
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Thank you for your fast reply.

    quast.py \
        $hap1 \
        $hap2 \
        --nanopore $fastq \
        -r ${params.genomeref} \
        -o quast_diploid \
        --threads $task.cpus

This is the command that I have used to run quast, but at the beginning of the log file you can see the exact files and their corresponding formats. The docker version is the latest one, for the 5.2.0 version.

Unfortunately no error message has been shown, from the log the process seems to have finished without problems.

@Kincekara
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Hi @ChiaraCampanelli,
It is tough to say anything without seeing an error log. Can you reach the following file?

/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast.log

@ChiaraCampanelli
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This is the log file you asked.

/quast-5.2.0/quast.py hapdup_phased_1.fasta hapdup_phased_2.fasta --nanopore BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq -r /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -o quast_diploid --threads 36

Version: 5.2.0

System information:
  OS: Linux-4.18.0-425.13.1.el8_7.x86_64-x86_64-with-Ubuntu-20.04-focal (linux_64)
  Python version: 2.7.18
  CPUs number: 72

Started: 2023-11-23 15:55:41

Logging to /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast.log

CWD: /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf
Main parameters: 
  MODE: default, threads: 36, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Reference:
  /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna ==> GCA_000001405.15_GRCh38_no_alt_analysis_set

Contigs:
  Pre-processing...
  1  hapdup_phased_1.fasta ==> hapdup_phased_1
  2  hapdup_phased_2.fasta ==> hapdup_phased_2

2023-11-23 15:59:44
Running Reads analyzer...
  Logging to files /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.log and /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err...
  Will not search Structural Variations (needs paired-end reads)
  1  Pre-processing reads...
  1  Running BWA...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
  2  Pre-processing reads...
  2  Running BWA...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
  Pre-processing reads...
  Running BWA for reference...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 12 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> hapdup_phased_1.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 12 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> hapdup_phased_2.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 12 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> GCA_000001405.15_GRCh38_no_alt_analysis_set.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
The tool returned non-zero. See ../reads_stats.err for stderr.
/quast-5.2.0/quast_libs/sambamba/sambamba_linux view -t 12 -h -S -f bam hapdup_phased_2.nanopore1.sam \
> hapdup_phased_2.nanopore1.bam 2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
  2  Done.
/quast-5.2.0/quast_libs/sambamba/sambamba_linux view -H -S quast_diploid/reads_stats/temp_output/hapdup_phased_2.sam \
> quast_diploid/reads_stats/hapdup_phased_2.sam.header 2>> quast_diploid/reads_stats/reads_stats.err
  2  Sorting SAM-file...
/quast-5.2.0/quast_libs/sambamba/sambamba_linux view -t 12 -h -S -f bam quast_diploid/reads_stats/temp_output/hapdup_phased_2.all.correct.sam \
> quast_diploid/reads_stats/temp_output/hapdup_phased_2.bam 2>> quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/sambamba/sambamba_linux flagstat -t 12 quast_diploid/reads_stats/temp_output/hapdup_phased_2.bam \
> quast_diploid/reads_stats/hapdup_phased_2.stat 2>> quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/bedtools/bin/bedtools bamtobed -i quast_diploid/reads_stats/temp_output/hapdup_phased_2.bam \
> quast_diploid/reads_stats/temp_output/hapdup_phased_2.bed 2>> quast_diploid/reads_stats/reads_stats.err
sort -k1,1 -k2,2n quast_diploid/reads_stats/temp_output/hapdup_phased_2.bed > quast_diploid/reads_stats/temp_output/hapdup_phased_2.sorted.bed \
2>> quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/bedtools/bin/bedtools genomecov -i quast_diploid/reads_stats/temp_output/hapdup_phased_2.sorted.bed \
-g quast_diploid/quast_corrected_input/hapdup_phased_2.fasta.fai > quast_diploid/reads_stats/temp_output/hapdup_phased_2.genomecov \
2>> quast_diploid/reads_stats/reads_stats.err
  2  Analysis is finished.

Let me know if you want me to attach the files quast is using.

@kapsakcj
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kapsakcj commented Nov 29, 2023 •
edited

I think I spotted the non-zero exit code/error:

/quast-5.2.0/quast_libs/minimap2/minimap2 -t 12 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
/lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> GCA_000001405.15_GRCh38_no_alt_analysis_set.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err
The tool returned non-zero. See ../reads_stats.err for stderr.

I think you'll need to look at this file to see the minimap2 error: /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/reads_stats/reads_stats.err. Can you share what it says?

@ChiaraCampanelli
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ChiaraCampanelli commented Nov 30, 2023 •
edited 

[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 20.42 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5781605530, availableWord=418815084
20.43 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5781526376, availableWord=418809524
22.65 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6199845082, availableWord=448243540
[BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed.
[BWTIncConstructFromPacked] 10 iterations done. 99999992 characters processed.
[BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed.
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[BWTIncConstructFromPacked] 440 iterations done. 4399999994 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999992 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999994 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999994 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999992 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999994 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999994 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999992 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999994 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999994 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999992 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999994 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999994 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999992 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999994 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999994 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999992 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999994 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999994 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999992 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999994 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999994 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999992 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999994 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5195016362 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5195008424 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999994 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5279476826 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5279460952 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999994 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5354541466 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5354518584 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5199999994 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5421255098 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5421225976 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5480546362 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5480511672 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5299999994 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5533240570 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5533200920 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5399999994 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5580071322 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5580027272 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5621690554 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5621642600 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5499999994 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5658677834 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5658626376 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5691548186 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5691493624 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5596764458 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5720759370 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5720702120 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 5746718314 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 5746658664 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 5769786666 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5683075690 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 5769724856 characters processed.
[bwa_index] 2046.04 seconds elapse.
[bwa_index] Update BWT... [bwa_index] 2049.27 seconds elapse.
[bwa_index] Update BWT... 15.21 sec
[bwa_index] Pack forward-only FASTA... 15.00 sec
[bwa_index] Pack forward-only FASTA... [BWTIncConstructFromPacked] 580 iterations done. 5759785322 characters processed.
13.94 sec
[bwa_index] Construct SA from BWT and Occ... 13.89 sec
[bwa_index] Construct SA from BWT and Occ... [BWTIncConstructFromPacked] 590 iterations done. 5827961034 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5888551818 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5942400986 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5990258282 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6032789930 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6070588138 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6104179258 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6134031130 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6160559482 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6184133946 characters processed.
[bwa_index] 2297.89 seconds elapse.
[bwa_index] Update BWT... 16.67 sec
[bwa_index] Pack forward-only FASTA... 15.53 sec
[bwa_index] Construct SA from BWT and Occ... 662.13 sec
[bwt_gen] Finished constructing BWT in 646 iterations.
[main] Version: 0.7.15-r1140
[main] CMD: /quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta -a bwtsw /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta
[main] Real time: 2770.259 sec; CPU: 2757.475 sec
662.63 sec
[bwt_gen] Finished constructing BWT in 646 iterations.
[main] Version: 0.7.15-r1140
[main] CMD: /quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta -a bwtsw /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta
[main] Real time: 2770.566 sec; CPU: 2761.485 sec
[M::mm_idx_gen::54.914*1.50] collected minimizers
[M::mm_idx_gen::54.715*1.51] collected minimizers
[M::mm_idx_gen::59.093*2.24] sorted minimizers
[M::main::59.095*2.24] loaded/built the index for 13468 target sequence(s)
[M::mm_idx_gen::58.893*2.24] sorted minimizers
[M::main::58.904*2.24] loaded/built the index for 13462 target sequence(s)
[M::mm_mapopt_update::60.441*2.21] mid_occ = 662
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 13468
[M::mm_mapopt_update::60.864*2.20] mid_occ = 661
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 13462
[M::mm_idx_stat::61.639*2.18] distinct minimizers: 99844347 (38.99% are singletons); average occurrences: 5.449; average spacing: 5.313; total length: 2890802765
[M::mm_idx_stat::62.052*2.18] distinct minimizers: 99845017 (38.99% are singletons); average occurrences: 5.449; average spacing: 5.313; total length: 2890763188
[M::worker_pipeline::273.144*7.42] mapped 42100 sequences
[M::worker_pipeline::274.632*7.41] mapped 42100 sequences
713.92 sec
[bwt_gen] Finished constructing BWT in 688 iterations.
[main] Version: 0.7.15-r1140
[main] CMD: /quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -a bwtsw /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
[main] Real time: 3075.877 sec; CPU: 3066.670 sec
[M::mm_idx_gen::59.979*1.48] collected minimizers
[M::mm_idx_gen::64.621*2.21] sorted minimizers
[M::main::64.622*2.21] loaded/built the index for 195 target sequence(s)
[M::mm_mapopt_update::66.536*2.17] mid_occ = 694
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 195
[M::mm_idx_stat::67.743*2.15] distinct minimizers: 100167746 (38.80% are singletons); average occurrences: 5.519; average spacing: 5.607; total length: 3099922541
[M::worker_pipeline::445.642*9.03] mapped 40650 sequences
[M::worker_pipeline::240.897*8.96] mapped 42100 sequences
[M::worker_pipeline::595.054*9.61] mapped 45117 sequences
[M::worker_pipeline::429.072*10.22] mapped 40650 sequences
[M::worker_pipeline::751.917*9.92] mapped 44773 sequences
[M::worker_pipeline::892.323*10.22] mapped 46292 sequences
[M::worker_pipeline::599.828*10.58] mapped 45117 sequences
[M::worker_pipeline::1048.080*10.38] mapped 43805 sequences
[M::worker_pipeline::767.483*10.80] mapped 44773 sequences
[M::worker_pipeline::1188.809*10.56] mapped 45925 sequences
[M::worker_pipeline::925.470*10.95] mapped 46292 sequences
[M::worker_pipeline::1346.429*10.64] mapped 46143 sequences
[M::worker_pipeline::1091.119*11.03] mapped 43805 sequences
[M::worker_pipeline::1498.356*10.78] mapped 45339 sequences
[M::worker_pipeline::1239.767*11.13] mapped 45925 sequences
[M::worker_pipeline::1644.453*10.85] mapped 46327 sequences
[M::worker_pipeline::1400.508*11.21] mapped 46143 sequences
[M::worker_pipeline::1787.303*10.93] mapped 46119 sequences
[M::worker_pipeline::1563.452*11.26] mapped 45339 sequences
[M::worker_pipeline::1952.153*10.99] mapped 43271 sequences
[M::worker_pipeline::1726.176*11.26] mapped 46327 sequences
[M::worker_pipeline::2109.628*11.02] mapped 45442 sequences
[M::worker_pipeline::1875.228*11.31] mapped 46119 sequences
[M::worker_pipeline::2257.565*11.05] mapped 47045 sequences
[M::worker_pipeline::2040.326*11.36] mapped 43271 sequences
[M::worker_pipeline::2403.170*11.09] mapped 45708 sequences
[M::worker_pipeline::2212.811*11.35] mapped 45442 sequences
[M::worker_pipeline::2544.414*11.13] mapped 45755 sequences
[M::worker_pipeline::2366.290*11.37] mapped 47045 sequences
[M::worker_pipeline::2695.449*11.15] mapped 45365 sequences
[M::worker_pipeline::2521.851*11.39] mapped 45708 sequences
[M::worker_pipeline::2841.578*11.17] mapped 43983 sequences
[M::worker_pipeline::2675.696*11.42] mapped 45755 sequences
[M::worker_pipeline::2986.684*11.21] mapped 44224 sequences
[M::worker_pipeline::3131.531*11.24] mapped 45646 sequences
[M::worker_pipeline::2834.958*11.44] mapped 45365 sequences
[M::worker_pipeline::3278.102*11.27] mapped 43411 sequences
[M::worker_pipeline::2989.033*11.45] mapped 43983 sequences
[M::worker_pipeline::3430.669*11.30] mapped 45259 sequences
[M::worker_pipeline::3153.699*11.48] mapped 44224 sequences
[M::worker_pipeline::3576.352*11.29] mapped 45451 sequences
[M::worker_pipeline::3312.242*11.48] mapped 45646 sequences
[M::worker_pipeline::3722.180*11.31] mapped 44556 sequences
[M::worker_pipeline::3479.245*11.48] mapped 43411 sequences
[M::worker_pipeline::3863.409*11.33] mapped 44393 sequences
[M::worker_pipeline::3645.639*11.48] mapped 45259 sequences
[M::worker_pipeline::4016.562*11.33] mapped 44907 sequences
[M::worker_pipeline::3797.488*11.49] mapped 45451 sequences
[M::worker_pipeline::4159.392*11.35] mapped 45496 sequences
[M::worker_pipeline::3956.394*11.51] mapped 44556 sequences
[M::worker_pipeline::4301.809*11.36] mapped 43225 sequences
[M::worker_pipeline::4109.327*11.52] mapped 44393 sequences
[M::worker_pipeline::4457.450*11.37] mapped 44964 sequences
[M::worker_pipeline::4281.374*11.51] mapped 44907 sequences
[M::worker_pipeline::4608.501*11.38] mapped 42738 sequences
[M::worker_pipeline::4436.649*11.51] mapped 45496 sequences
[M::worker_pipeline::4767.476*11.39] mapped 42989 sequences
[M::worker_pipeline::4595.560*11.52] mapped 43225 sequences
[M::worker_pipeline::4911.436*11.40] mapped 44652 sequences
[M::worker_pipeline::4758.337*11.53] mapped 44964 sequences
[M::worker_pipeline::5074.787*11.40] mapped 45080 sequences
[M::worker_pipeline::5226.330*11.39] mapped 43070 sequences
[M::worker_pipeline::4928.107*11.52] mapped 42738 sequences
[M::worker_pipeline::5376.832*11.40] mapped 43924 sequences
[M::worker_pipeline::5090.971*11.53] mapped 42989 sequences
[M::worker_pipeline::5524.195*11.40] mapped 45225 sequences
[M::worker_pipeline::5245.012*11.54] mapped 44652 sequences
[M::worker_pipeline::5678.942*11.41] mapped 44376 sequences
[M::worker_pipeline::5412.363*11.54] mapped 45080 sequences
[M::worker_pipeline::5838.161*11.40] mapped 46352 sequences
[M::worker_pipeline::5574.469*11.54] mapped 43070 sequences
[M::worker_pipeline::5985.697*11.40] mapped 46041 sequences
[M::worker_pipeline::5739.582*11.53] mapped 43924 sequences
[M::worker_pipeline::6141.561*11.40] mapped 46304 sequences
[M::worker_pipeline::5898.757*11.53] mapped 45225 sequences
[M::worker_pipeline::6294.668*11.40] mapped 44657 sequences
[M::worker_pipeline::6057.082*11.54] mapped 44376 sequences
[M::worker_pipeline::6439.648*11.41] mapped 44042 sequences
[M::worker_pipeline::6225.502*11.52] mapped 46352 sequences
[M::worker_pipeline::6584.441*11.42] mapped 43958 sequences
[M::worker_pipeline::6387.325*11.52] mapped 46041 sequences
[M::worker_pipeline::6737.192*11.42] mapped 43573 sequences
[M::worker_pipeline::6543.575*11.53] mapped 46304 sequences
[M::worker_pipeline::6886.067*11.43] mapped 43340 sequences
[M::worker_pipeline::6702.944*11.53] mapped 44657 sequences
[M::worker_pipeline::7046.471*11.43] mapped 45381 sequences
[M::worker_pipeline::6849.515*11.54] mapped 44042 sequences
[M::worker_pipeline::7195.965*11.44] mapped 45650 sequences
[M::worker_pipeline::7001.900*11.55] mapped 43958 sequences
[M::worker_pipeline::7357.272*11.43] mapped 42209 sequences
[M::worker_pipeline::7156.104*11.55] mapped 43573 sequences
[M::worker_pipeline::7510.925*11.43] mapped 42379 sequences
[M::worker_pipeline::7318.532*11.56] mapped 43340 sequences
[M::worker_pipeline::7652.847*11.44] mapped 46851 sequences
[M::worker_pipeline::7475.755*11.56] mapped 45381 sequences
[M::worker_pipeline::7804.671*11.44] mapped 44823 sequences
[M::worker_pipeline::7634.001*11.56] mapped 45650 sequences
[M::worker_pipeline::7960.970*11.45] mapped 43170 sequences
[M::worker_pipeline::8111.163*11.45] mapped 43522 sequences
[M::worker_pipeline::7804.898*11.56] mapped 42209 sequences
[M::worker_pipeline::8258.257*11.46] mapped 46131 sequences
[M::worker_pipeline::7969.629*11.55] mapped 42379 sequences
[M::worker_pipeline::8407.663*11.46] mapped 44666 sequences
[M::worker_pipeline::8124.536*11.56] mapped 46851 sequences
[M::worker_pipeline::8557.314*11.46] mapped 46401 sequences
[M::worker_pipeline::8282.106*11.56] mapped 44823 sequences
[M::worker_pipeline::8707.343*11.46] mapped 44936 sequences
[M::worker_pipeline::8443.904*11.57] mapped 43170 sequences
[M::worker_pipeline::8861.491*11.47] mapped 44735 sequences
[M::worker_pipeline::8605.368*11.57] mapped 43522 sequences
[M::worker_pipeline::9017.167*11.47] mapped 45228 sequences
[M::worker_pipeline::8755.930*11.57] mapped 46131 sequences
[M::worker_pipeline::9184.172*11.46] mapped 43594 sequences
[M::worker_pipeline::8917.455*11.57] mapped 44666 sequences
[M::worker_pipeline::9330.925*11.46] mapped 44173 sequences
[M::worker_pipeline::9080.863*11.57] mapped 46401 sequences
[M::worker_pipeline::9475.246*11.47] mapped 44378 sequences
[M::worker_pipeline::9247.344*11.57] mapped 44936 sequences
[M::worker_pipeline::9626.053*11.47] mapped 46338 sequences
[M::worker_pipeline::9407.919*11.57] mapped 44735 sequences
[M::worker_pipeline::9779.625*11.48] mapped 45984 sequences
[M::worker_pipeline::9565.792*11.58] mapped 45228 sequences
[M::worker_pipeline::9932.790*11.48] mapped 45543 sequences
[M::worker_pipeline::9728.864*11.58] mapped 43594 sequences
[M::worker_pipeline::10074.499*11.48] mapped 46613 sequences
[M::worker_pipeline::9876.691*11.59] mapped 44173 sequences
[M::worker_pipeline::10220.626*11.48] mapped 45068 sequences
[M::worker_pipeline::10042.576*11.59] mapped 44378 sequences
[M::worker_pipeline::10376.841*11.48] mapped 44657 sequences
[M::worker_pipeline::10196.678*11.59] mapped 46338 sequences
[M::worker_pipeline::10523.576*11.48] mapped 44832 sequences
[M::worker_pipeline::10357.022*11.59] mapped 45984 sequences
[M::worker_pipeline::10679.592*11.47] mapped 48611 sequences
[M::worker_pipeline::10818.387*11.48] mapped 44379 sequences
[M::worker_pipeline::10514.292*11.60] mapped 45543 sequences
[M::worker_pipeline::10975.060*11.48] mapped 44903 sequences
[M::worker_pipeline::10672.299*11.60] mapped 46613 sequences
[M::worker_pipeline::11126.983*11.48] mapped 45063 sequences
[M::worker_pipeline::10827.670*11.61] mapped 45068 sequences
[M::worker_pipeline::11276.308*11.49] mapped 41903 sequences
[M::worker_pipeline::10988.981*11.61] mapped 44657 sequences
[M::worker_pipeline::11428.507*11.49] mapped 43989 sequences
[M::worker_pipeline::11149.212*11.61] mapped 44832 sequences
[M::worker_pipeline::11579.994*11.50] mapped 45285 sequences
[M::worker_pipeline::11327.304*11.60] mapped 48611 sequences
[M::worker_pipeline::11731.895*11.50] mapped 44755 sequences
[M::worker_pipeline::11482.659*11.60] mapped 44379 sequences
[M::worker_pipeline::11879.587*11.50] mapped 43052 sequences
[M::worker_pipeline::11643.654*11.61] mapped 44903 sequences
[M::worker_pipeline::12024.518*11.51] mapped 46207 sequences
[M::worker_pipeline::11800.667*11.61] mapped 45063 sequences
[M::worker_pipeline::12166.555*11.51] mapped 43673 sequences
[M::worker_pipeline::11962.679*11.61] mapped 41903 sequences
[M::worker_pipeline::12321.545*11.51] mapped 43712 sequences
[M::worker_pipeline::12128.768*11.60] mapped 43989 sequences
[M::worker_pipeline::12484.303*11.51] mapped 45067 sequences
[M::worker_pipeline::12283.489*11.61] mapped 45285 sequences
[M::worker_pipeline::12619.667*11.51] mapped 46077 sequences
[M::worker_pipeline::12446.498*11.61] mapped 44755 sequences
[M::worker_pipeline::12764.823*11.51] mapped 46028 sequences
[M::worker_pipeline::12599.533*11.61] mapped 43052 sequences
[M::worker_pipeline::12911.444*11.52] mapped 44997 sequences
[M::worker_pipeline::12752.644*11.62] mapped 46207 sequences
[M::worker_pipeline::13063.717*11.51] mapped 44743 sequences
[M::worker_pipeline::13210.143*11.51] mapped 44266 sequences
[M::worker_pipeline::12914.423*11.61] mapped 43673 sequences
[M::worker_pipeline::13371.456*11.51] mapped 43393 sequences
[M::worker_pipeline::13067.311*11.62] mapped 43712 sequences
[M::worker_pipeline::13510.411*11.51] mapped 43394 sequences
[M::worker_pipeline::13232.774*11.62] mapped 45067 sequences
[M::worker_pipeline::13656.750*11.51] mapped 44656 sequences
[M::worker_pipeline::13382.304*11.62] mapped 46077 sequences
[M::worker_pipeline::13815.251*11.51] mapped 42833 sequences
[M::worker_pipeline::13540.511*11.62] mapped 46028 sequences
[M::worker_pipeline::13972.545*11.51] mapped 49113 sequences
[M::worker_pipeline::13694.060*11.63] mapped 44997 sequences
[M::worker_pipeline::14118.244*11.52] mapped 45048 sequences
[M::worker_pipeline::13850.969*11.63] mapped 44743 sequences
[M::worker_pipeline::14265.663*11.52] mapped 48377 sequences
[M::worker_pipeline::14007.896*11.63] mapped 44266 sequences
[M::worker_pipeline::14418.049*11.52] mapped 49920 sequences
[M::worker_pipeline::14176.772*11.63] mapped 43393 sequences
[M::worker_pipeline::14563.574*11.52] mapped 48322 sequences
[M::worker_pipeline::14332.172*11.63] mapped 43394 sequences
[M::worker_pipeline::14728.214*11.52] mapped 45962 sequences
[M::worker_pipeline::14496.003*11.62] mapped 44656 sequences
[M::worker_pipeline::14881.830*11.52] mapped 47572 sequences
[M::worker_pipeline::14660.188*11.63] mapped 42833 sequences
[M::worker_pipeline::15041.666*11.52] mapped 50810 sequences
[M::worker_pipeline::14827.812*11.62] mapped 49113 sequences
[M::worker_pipeline::15199.706*11.52] mapped 45680 sequences
[M::worker_pipeline::14989.802*11.62] mapped 45048 sequences
[M::worker_pipeline::15348.530*11.52] mapped 46481 sequences
[M::worker_pipeline::15147.738*11.63] mapped 48377 sequences
[M::worker_pipeline::15501.682*11.52] mapped 51909 sequences
[M::worker_pipeline::15309.525*11.62] mapped 49920 sequences
[M::worker_pipeline::15635.537*11.53] mapped 69345 sequences
[M::worker_pipeline::15762.378*11.53] mapped 75262 sequences
[M::worker_pipeline::15468.883*11.63] mapped 48322 sequences
[M::worker_pipeline::15893.954*11.53] mapped 69047 sequences
[M::worker_pipeline::15634.331*11.62] mapped 45962 sequences
[M::worker_pipeline::16027.089*11.53] mapped 72184 sequences
[M::worker_pipeline::15792.494*11.63] mapped 47572 sequences
[M::worker_pipeline::16160.715*11.53] mapped 69936 sequences
[M::worker_pipeline::15966.329*11.62] mapped 50810 sequences
[M::worker_pipeline::16284.122*11.53] mapped 72486 sequences
[M::worker_pipeline::16410.541*11.54] mapped 70194 sequences
[M::worker_pipeline::16127.410*11.63] mapped 45680 sequences
[M::worker_pipeline::16538.570*11.54] mapped 73350 sequences
[M::worker_pipeline::16297.300*11.62] mapped 46481 sequences
[M::worker_pipeline::16667.395*11.54] mapped 67983 sequences
[M::worker_pipeline::16462.169*11.62] mapped 51909 sequences
[M::worker_pipeline::16794.983*11.54] mapped 70946 sequences
[M::worker_pipeline::16599.204*11.62] mapped 69345 sequences
[M::worker_pipeline::16925.916*11.54] mapped 80214 sequences
[M::worker_pipeline::16733.409*11.62] mapped 75262 sequences
[M::worker_pipeline::17046.789*11.55] mapped 69017 sequences
[M::worker_pipeline::16869.006*11.63] mapped 69047 sequences
[M::worker_pipeline::17177.962*11.55] mapped 69219 sequences
[M::worker_pipeline::17007.867*11.63] mapped 72184 sequences
[M::worker_pipeline::17320.729*11.55] mapped 70478 sequences
[M::worker_pipeline::17448.982*11.55] mapped 64771 sequences
[M::worker_pipeline::17154.833*11.63] mapped 69936 sequences
[M::worker_pipeline::17575.154*11.55] mapped 70299 sequences
[M::worker_pipeline::17291.164*11.63] mapped 72486 sequences
[M::worker_pipeline::17703.420*11.55] mapped 69638 sequences
[M::worker_pipeline::17425.900*11.63] mapped 70194 sequences
[M::worker_pipeline::17833.433*11.55] mapped 77892 sequences
[M::worker_pipeline::17563.292*11.63] mapped 73350 sequences
[M::worker_pipeline::17961.205*11.55] mapped 72975 sequences
[M::worker_pipeline::17705.571*11.64] mapped 67983 sequences
[M::worker_pipeline::18094.381*11.56] mapped 66091 sequences
[M::worker_pipeline::17844.303*11.64] mapped 70946 sequences
[M::worker_pipeline::18222.539*11.56] mapped 68082 sequences
[M::worker_pipeline::17977.597*11.64] mapped 80214 sequences
[M::worker_pipeline::18353.828*11.56] mapped 67062 sequences
[M::worker_pipeline::18111.933*11.64] mapped 69017 sequences
[M::worker_pipeline::18488.423*11.56] mapped 75238 sequences
[M::worker_pipeline::18250.497*11.64] mapped 69219 sequences
[M::worker_pipeline::18631.469*11.56] mapped 66302 sequences
[M::worker_pipeline::18391.166*11.64] mapped 70478 sequences

It seems ok?

@Kincekara
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It looks like the quast stopped abruptly. "Analysis is finished." prompt is for an individual step. Your working directory is /lustre1/project/stg_00124/Chiara/tmp/88/2f836d3cdf8087578641b1eccbeccf/quast_diploid/
If created, you should be able to find any results in error logs in that directory. I don't think this is a docker-related issue. You can try setting threads manually to avoid hardware-specific problems.

@kapsakcj
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Hmm I wonder if maybe the mapping process didn't finish or ran out of memory or something. Usually you will see some kind of confirmation message that the mapping has finished.

Have you re-ran with less CPUs? or request more RAM on the SLURM runner?

@ChiaraCampanelli
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Thank you for your help.
I lowered the CPU capacity and kept high the RAM as you suggested. I will let you know as soon as it will finish, unfortunately the cluster is very slow these days.
Regarding the number of threads, it's already manually set according to the number of task.

@ChiaraCampanelli
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Unfortunately there are no progresses, despite I have changed the resources as you suggested.

/quast-5.2.0/quast.py hapdup_phased_1.fasta hapdup_phased_2.fasta --nanopore BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq -r /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -o quast_diploid --threads 8

Version: 5.2.0

System information:
  OS: Linux-4.18.0-425.13.1.el8_7.x86_64-x86_64-with-Ubuntu-20.04-focal (linux_64)
  Python version: 2.7.18
  CPUs number: 72

Started: 2023-11-30 23:27:24

Logging to /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast.log

CWD: /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1
Main parameters: 
  MODE: default, threads: 8, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Reference:
  /staging/leuven/stg_00019/research/nextflowPipeline/Resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna ==> GCA_000001405.15_GRCh38_no_alt_analysis_set

Contigs:
  Pre-processing...
  1  hapdup_phased_1.fasta ==> hapdup_phased_1
  2  hapdup_phased_2.fasta ==> hapdup_phased_2

2023-11-30 23:54:48
Running Reads analyzer...
  Logging to files /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.log and /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err...
  Will not search Structural Variations (needs paired-end reads)
  2  Pre-processing reads...
  2  Running BWA...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err
  1  Pre-processing reads...
  1  Running BWA...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err
  Pre-processing reads...
  Running BWA for reference...
/quast-5.2.0/quast_libs/bwa/bwa index -p /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-a bwtsw >> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err \
2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 2 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_2.fasta \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> hapdup_phased_2.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 2 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/hapdup_phased_1.fasta \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> hapdup_phased_1.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err
/quast-5.2.0/quast_libs/minimap2/minimap2 -t 2 -ax map-ont /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/quast_corrected_input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
/lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/BGB_GC136541_all_runs_mrl8_kmer10_final_trimmed.fastq \
> GCA_000001405.15_GRCh38_no_alt_analysis_set.nanopore1.sam 2>> /lustre1/project/stg_00124/Chiara/tmp/8b/fb83af95448a62766a8477cce859d1/quast_diploid/reads_stats/reads_stats.err

As often happens, the analysis got stuck in the BWA run phase. It's been almost 20 hours that is working without updates.

@kapsakcj
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kapsakcj commented Dec 1, 2023

I'm not sure what else to suggest here, as I don't typically run quast this way.

You could try using a biocontainer docker image for quast, and that would help determine if the issue is caused by the staphb docker image or not.

Try the most recent v5.2.0 image from here? https://quay.io/repository/biocontainers/quast?tab=tags

If you get the same behavior with the biocontainer docker image, that might mean there's something wrong with your input files or some other cause

@Kincekara Kincekara assigned Kincekara and unassigned Kincekara Dec 1, 2023
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@kapsakcj @Kincekara @ChiaraCampanelli