Require for Singularity image of Clair3

[huangnengCSU]

Hi,
Since HPC can not support docker, could you provide the singularity image and running example. I converted the docker image to a singularity image and successfully ran run_clair3.sh --help. However, when I tried to call variants, it always outputs the error message as follows:

[hpc_hn@node0023 120G]$ singularity exec --bind /public/home/hpc_hn/ont-quickstart/input/120G ~/tools/clair_docker_image/clair3_docker_image.sif /opt/bin/run_clair3.sh -b /public/home/hpc_hn/ont-quickstart/input/120G/hg003_120G.bam -f /public/home/hpc_hn/ont-quickstart/input/120G/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna -t 2 -p ont -m /public/home/hpc_hn/ont-quickstart/input/120G/ont -o /public/home/hpc_hn/ont-quickstart/input/120G/output
[INFO] BAM FILE PATH: /public/home/hpc_hn/ont-quickstart/input/120G/hg003_120G.bam
[INFO] REFERENCE FILE PATH: /public/home/hpc_hn/ont-quickstart/input/120G/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna
[INFO] MODEL PATH: /public/home/hpc_hn/ont-quickstart/input/120G/ont
[INFO] OUTPUT FOLDER: /public/home/hpc_hn/ont-quickstart/input/120G/output
[INFO] PLATFORM: ont
[INFO] THREADS: 2
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: EMPTY
[INFO] SAMTOOLS PATH: samtools
[INFO] PYTHON PATH: python3
[INFO] PYPY PATH: pypy3
[INFO] PARALLEL PATH: parallel
[INFO] WHATSHAP PATH: whatshap
[INFO] CHUNK SIZE: 5000000
[INFO] CHUNK NUM: 0
[INFO] FULL ALIGN PROPORTION: 0.3
[INFO] FULL ALIGN RERFERENCE PROPORTION: 0.3
[INFO] USER DEFINED SNP THRESHOLD: 0.0
[INFO] USER DEFINED INDEL THRESHOLD: 0.0
[INFO] ENABLE FILEUP ONLY CALLING: False
[INFO] ENABLE FAST MODE CALLING: False
[INFO] ENABLE PRINTING REFERENCE CALLS: False
[INFO] ENABLE OUTPUT GVCF: False
[INFO] ENABLE HAPLOID PRECISE MODE: False
[INFO] ENABLE HAPLOID SENSITIVE MODE: False
[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False

+ /opt/bin/scripts/clair3.sh --bam_fn /public/home/hpc_hn/ont-quickstart/input/120G/hg003_120G.bam --ref_fn /public/home/hpc_hn/ont-quickstart/input/120G/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --threads 2 --model_path /public/home/hpc_hn/ont-quickstart/input/120G/ont --platform ont --output /public/home/hpc_hn/ont-quickstart/input/120G/output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=EMPTY --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=0 --var_pct_full=0.3 --ref_pct_full=0.3 --snp_min_af=0.0 --indel_min_af=0.0 --pileup_only=False --gvcf=False --fast_mode=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False
[INFO] Check envrionment variables
[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default
[INFO] Call variant in contigs: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY
[INFO] Chunk number for each contig: 50 49 40 39 37 35 32 30 28 27 28 27 23 22 21 19 17 17 12 13 10 11 32 12
[INFO] 1/7 Calling variants using pileup model
[INFO] Delay 7 seconds before starting variant calling ...
taskset: failed to set pid 0's affinity: Invalid argument
[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
  File "/opt/bin/clair3/../clair3.py", line 89, in <module>
    main()
  File "/opt/bin/clair3/../clair3.py", line 83, in main
    submodule.main()
  File "/opt/bin/preprocess/CreateTensorPileup.py", line 550, in main
    CreateTensorPileup(args)
  File "/opt/bin/preprocess/CreateTensorPileup.py", line 414, in CreateTensorPileup
    tensor_can_fp.stdin.write(l)
BrokenPipeError: [Errno 32] Broken pipe

[aquaskyline]

Seems the taskset command is missing in your running environment, not sure if it's a problem of singularity or not. We are now looking into the problem and will turn back to you with a solution asap.

[huangnengCSU]

@aquaskyline
I have checked the environment and the taskset version is util-linux 2.23.2. And I installed Clair3 using conda and ran the command, it outputs the same error.

bash ~/tools/Clair3/run_clair3.sh -b `pwd`/hg003_120G.bam -f `pwd`/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna -m /public/home/hpc_hn/tools/Clair3/models/ont/ -t 4 -p ont -o `pwd`/clair3_output

[INFO] BAM FILE PATH: /public/home/hpc_hn/ont-quickstart/input/120G/hg003_120G.bam
[INFO] REFERENCE FILE PATH: /public/home/hpc_hn/ont-quickstart/input/120G/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna
[INFO] MODEL PATH: /public/home/hpc_hn/tools/Clair3/models/ont/
[INFO] OUTPUT FOLDER: /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output
[INFO] PLATFORM: ont
[INFO] THREADS: 4
[INFO] BED FILE PATH: EMPTY
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: EMPTY
[INFO] SAMTOOLS PATH: samtools
[INFO] PYTHON PATH: python3
[INFO] PYPY PATH: pypy3
[INFO] PARALLEL PATH: parallel
[INFO] WHATSHAP PATH: whatshap
[INFO] CHUNK SIZE: 5000000
[INFO] CHUNK NUM: 0
[INFO] FULL ALIGN PROPORTION: 0.3
[INFO] FULL ALIGN RERFERENCE PROPORTION: 0.3
[INFO] USER DEFINED SNP THRESHOLD: 0.0
[INFO] USER DEFINED INDEL THRESHOLD: 0.0
[INFO] ENABLE FILEUP ONLY CALLING: False
[INFO] ENABLE FAST MODE CALLING: False
[INFO] ENABLE PRINTING REFERENCE CALLS: False
[INFO] ENABLE OUTPUT GVCF: False
[INFO] ENABLE HAPLOID PRECISE MODE: False
[INFO] ENABLE HAPLOID SENSITIVE MODE: False
[INFO] ENABLE INCLUDE ALL CTGS CALLING: False
[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False

+ /public/home/hpc_hn/tools/Clair3/scripts/clair3.sh --bam_fn /public/home/hpc_hn/ont-quickstart/input/120G/hg003_120G.bam --ref_fn /public/home/hpc_hn/ont-quickstart/input/120G/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --threads 4 --model_path /public/home/hpc_hn/tools/Clair3/models/ont/ --platform ont --output /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=EMPTY --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=0 --var_pct_full=0.3 --ref_pct_full=0.3 --snp_min_af=0.0 --indel_min_af=0.0 --pileup_only=False --gvcf=False --fast_mode=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=False --include_all_ctgs=False --no_phasing_for_fa=False
[INFO] Check envrionment variables
[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default
[INFO] Call variant in contigs: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY
[INFO] Chunk number for each contig: 50 49 40 39 37 35 32 30 28 27 28 27 23 22 21 19 17 17 12 13 10 11 32 12
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/log
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/pileup_output
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/merge_output
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/phase_output
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/gvcf_tmp_output
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/full_alignment_output
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/phase_output/phase_vcf
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/phase_output/phase_bam
[INFO] Create folder /public/home/hpc_hn/ont-quickstart/input/120G/clair3_output/tmp/full_alignment_output/candidate_bed
[INFO] 1/7 Calling variants using pileup model
[INFO] Delay 0 seconds before starting variant calling ...
taskset: failed to set pid 0's affinity: Invalid argument
call_variant.py exited with exceptions. Exiting...
[INFO] Delay 2 seconds before starting variant calling ...
taskset: failed to set pid 0's affinity: Invalid argument
call_variant.py exited with exceptions. Exiting...

[aquaskyline]

The error was caused because taskset is asking for CPU cores that were made invisible to it by singularity. Here is a similar issue with more detailed explanations util-linux/util-linux#413. We are fixing the problem and will make a singularity image available asap.

[aquaskyline]

taskset problem fixed, and a singularity image is provided (see README.md) in v0.1-r1.