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The --snp workflow is halted due to a mosdepth/bedtools error: "command not found" #116

Closed kleighwill closed 7 months ago

kleighwill commented 7 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.8.3

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

command is written inside of an sbatch script

#!/bin/bash
#SBATCH --job-name=nf_RAD74444381
#SBATCH --time=48:00:00
#SBATCH --partition=owners
#SBATCH -c 16
#SBATCH --mem=30GB
#SBATCH --mail-type=BEGIN,END,FAIL

module load biology nextflow
OUTPUT=/scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw
nextflow run epi2me-labs/wf-human-variation \
    -w ${OUTPUT}/workspace \
    -profile singularity \
    --snp \
    --bam /scratch/groups/greicius/RUSH_AD/data/RAD74444381/RAD74444381.dorado_hac_basecalled.methylated_5mcG_5hmCG.unaligned.bam \
    --bed /home/groups/greicius/RUSH_AD/pipeline/human_GRCh38_no_alt_analysis_set.trf.bed \
    --ref /scratch/groups/greicius/RUSH_AD/nextflow/GRCh38.fa \
    --basecaller_cfg 'dna_r10.4.1_e8.2_400bps_hac@v4.2.0'  \
    --sample_name RAD74444381 \
    --out_dir ${OUTPUT}

Workflow Execution - CLI Execution Profile

singularity

What happened?

I'm currently trying to run the pipeline with only the --snp flag for one participant's pod5 files that have already been basecalled (so the pipeline is starting with the basecalled but unaligned bam). Most of the processes are executing normally, but the mosdepth input process has failed with the error message below. Any assistance would be greatly appreciated--thanks!

Relevant log output

N E X T F L O W  ~  version 23.04.3
Launching `https://github.com/epi2me-labs/wf-human-variation` [desperate_northcutt] DSL2 - revision: 93a02af3ff [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-human-variation v1.8.3-g93a02af
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : desperate_northcutt
  containerEngine: singularity
  container      : ontresearch/wf-human-variation:sha0800eade05e4cbb75d45421633c78c4f6320b2f6
  launchDir      : /scratch/groups/greicius/RUSH_AD/nextflow
  workDir        : /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace
  projectDir     : /home/users/kleigh/.nextflow/assets/epi2me-labs/wf-human-variation
  userName       : kleigh
  profile        : singularity
  configFiles    : /home/users/kleigh/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config

Workflow Options
  snp            : true

Main options
  sample_name    : RAD74444381
  bam            : /scratch/groups/greicius/RUSH_AD/data/RAD74444381/RAD74444381.dorado_hac_basecalled.methylated_5mcG_5hmCG.unaligned.bam
  ref            : /scratch/groups/greicius/RUSH_AD/nextflow/GRCh38.fa
  basecaller_cfg : dna_r10.4.1_e8.2_400bps_hac@v4.2.0
  bed            : /home/groups/greicius/RUSH_AD/pipeline/human_GRCh38_no_alt_analysis_set.trf.bed
  out_dir        : /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-human-variation for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-human-variation v1.8.3-g93a02af.
--------------------------------------------------------------------------------
[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     -
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[-        ] process > getVersions                    -
[-        ] process > getParams                      -
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[-        ] process > lookup_clair3_model            -

[-        ] process > bam_ingress:samtools_index     -
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[-        ] process > cram_cache                     [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[-        ] process > getVersions                    [  0%] 0 of 1
[-        ] process > getParams                      [  0%] 0 of 1
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[-        ] process > lookup_clair3_model            -
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[-        ] process > report_snp:getVersions         -
[-        ] process > report_snp:getParams           [  0%] 0 of 1
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[-        ] process > publish_artifact               [  0%] 0 of 1

executor >  local (8)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [  0%] 0 of 1
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [  0%] 0 of 1
[74/36499a] process > getParams                      [  0%] 0 of 1
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [  0%] 0 of 1
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [  0%] 0 of 1
[63/ab14eb] process > report_snp:getParams           [  0%] 0 of 1
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [  0%] 0 of 1

executor >  local (8)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [  0%] 0 of 1
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [  0%] 0 of 1
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [  0%] 0 of 1
[63/ab14eb] process > report_snp:getParams           [  0%] 0 of 1
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [100%] 1 of 1

executor >  local (8)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [  0%] 0 of 1
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [  0%] 0 of 1
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [100%] 1 of 1

executor >  local (8)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [  0%] 0 of 1
[-        ] process > bam_ingress:check_for_align... -
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [100%] 1 of 1
Autoselected Clair3 model: r1041_e82_400bps_hac_v420

executor >  local (9)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [  0%] 0 of 1
[-        ] process > bam_ingress:cram_to_bam        -
[-        ] process > bam_ingress:minimap2_alignment -
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [100%] 1 of 1
Autoselected Clair3 model: r1041_e82_400bps_hac_v420

executor >  local (10)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [  0%] 0 of 1
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [  0%] 0 of 1
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[d2/6fabc6] process > publish_artifact (1)           [100%] 1 of 1
Autoselected Clair3 model: r1041_e82_400bps_hac_v420

executor >  local (13)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [  0%] 0 of 1
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[58/5e768e] process > publish_artifact (2)           [ 25%] 1 of 4

executor >  local (13)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [  0%] 0 of 1
[-        ] process > getGenome                      -
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[-        ] process > configure_jbrowse              -
[10/2ea491] process > publish_artifact (4)           [100%] 4 of 4

executor >  local (16)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[-        ] process > mosdepth_input                 -
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [ 80%] 4 of 5

executor >  local (17)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[71/747346] process > mosdepth_input (1)             [  0%] 0 of 1
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [ 80%] 4 of 5
Pulling Singularity image docker://ontresearch/wf-common:sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7 [cache /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity/ontresearch-wf-common-sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location

executor >  local (17)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[71/747346] process > mosdepth_input (1)             [  0%] 0 of 1
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [100%] 5 of 5
Pulling Singularity image docker://ontresearch/wf-common:sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7 [cache /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity/ontresearch-wf-common-sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location

executor >  local (17)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[71/747346] process > mosdepth_input (1)             [  0%] 0 of 1
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [100%] 5 of 5
Pulling Singularity image docker://ontresearch/wf-common:sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7 [cache /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity/ontresearch-wf-common-sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'mosdepth_input (1)'

Caused by:
  Process `mosdepth_input (1)` terminated with an error exit status (127)

Command executed:

  export REF_PATH=GRCh38.fa
  export MOSDEPTH_PRECISION=3
  # extract first 3 columns of input BED to prevent col 4 leaking as label into outputs [CW-1702]
  # and convert them into windows of the given size [CW-2015]
  # The workflow now sort the bed input, merge overlapping intervals and then build windows
  # preventing crash in downstream tools [CW-2247]
  sort -k 1,1 -k2,2n human_GRCh38_no_alt_analysis_set.trf.bed |             bedtools merge -i - |             bedtools makewindows -b - -w 25000 > cut.bed
  # Run mosdepth
  mosdepth         -x         -t 2         -b cut.bed         --thresholds 1,10,20,30         --no-per-base         RAD74444381         RAD74444381.cram

Command exit status:
  127

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
  .command.sh: line 8: bedtools: command not found
  .command.sh: line 8: bedtools: command not found

Work dir:
  /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/71/747346622176cf661c72ba80e338e0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

executor >  local (17)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[71/747346] process > mosdepth_input (1)             [100%] 1 of 1, failed: 1 ✘
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [100%] 5 of 5
Pulling Singularity image docker://ontresearch/wf-common:sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7 [cache /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity/ontresearch-wf-common-sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'mosdepth_input (1)'

Caused by:
  Process `mosdepth_input (1)` terminated with an error exit status (127)

Command executed:

  export REF_PATH=GRCh38.fa
  export MOSDEPTH_PRECISION=3
  # extract first 3 columns of input BED to prevent col 4 leaking as label into outputs [CW-1702]
  # and convert them into windows of the given size [CW-2015]
  # The workflow now sort the bed input, merge overlapping intervals and then build windows
  # preventing crash in downstream tools [CW-2247]
  sort -k 1,1 -k2,2n human_GRCh38_no_alt_analysis_set.trf.bed |             bedtools merge -i - |             bedtools makewindows -b - -w 25000 > cut.bed
  # Run mosdepth
  mosdepth         -x         -t 2         -b cut.bed         --thresholds 1,10,20,30         --no-per-base         RAD74444381         RAD74444381.cram

Command exit status:
  127

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
  .command.sh: line 8: bedtools: command not found
  .command.sh: line 8: bedtools: command not found

Work dir:
  /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/71/747346622176cf661c72ba80e338e0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

executor >  local (17)
[a7/0e3af3] process > bam_ingress:samtools_index (1) [100%] 1 of 1 ✔
[f6/bf79c0] process > bam_ingress:check_for_align... [100%] 1 of 1 ✔
[-        ] process > bam_ingress:cram_to_bam        -
[72/4be97f] process > bam_ingress:minimap2_alignm... [100%] 1 of 1 ✔
[7d/6bb868] process > getGenome (1)                  [  0%] 0 of 1
[ff/0e77f2] process > cram_cache (1)                 [100%] 1 of 1 ✔
[71/747346] process > mosdepth_input (1)             [100%] 1 of 1, failed: 1 ✘
[-        ] process > readStats                      -
[96/de4933] process > getVersions                    [100%] 1 of 1 ✔
[74/36499a] process > getParams                      [100%] 1 of 1 ✔
[-        ] process > get_region_coverage            -
[-        ] process > makeAlignmentReport            -
[-        ] process > failedQCReport                 -
[6f/601bd8] process > lookup_clair3_model (1)        [100%] 1 of 1 ✔
[-        ] process > snp:make_chunks                -
[-        ] process > snp:pileup_variants            -
[-        ] process > snp:aggregate_pileup_variants  -
[-        ] process > snp:select_het_snps            -
[-        ] process > snp:phase_contig               -
[-        ] process > snp:get_qual_filter            -
[-        ] process > snp:create_candidates          -
[-        ] process > snp:evaluate_candidates        -
[-        ] process > snp:aggregate_full_align_va... -
[-        ] process > snp:merge_pileup_and_full_vars -
[-        ] process > snp:aggregate_all_variants     -
[-        ] process > bed_filter                     -
[-        ] process > annotate_snp_vcf               -
[-        ] process > vcfStats                       -
[a1/6cffa1] process > report_snp:getVersions         [100%] 1 of 1 ✔
[63/ab14eb] process > report_snp:getParams           [100%] 1 of 1 ✔
[-        ] process > report_snp:makeReport          -
[-        ] process > output_snp                     -
[3f/ba6fc4] process > configure_jbrowse (1)          [  0%] 0 of 1
[9a/c0c941] process > publish_artifact (5)           [100%] 5 of 5
Pulling Singularity image docker://ontresearch/wf-common:sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7 [cache /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity/ontresearch-wf-common-sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'mosdepth_input (1)'

Caused by:
  Process `mosdepth_input (1)` terminated with an error exit status (127)

Command executed:

  export REF_PATH=GRCh38.fa
  export MOSDEPTH_PRECISION=3
  # extract first 3 columns of input BED to prevent col 4 leaking as label into outputs [CW-1702]
  # and convert them into windows of the given size [CW-2015]
  # The workflow now sort the bed input, merge overlapping intervals and then build windows
  # preventing crash in downstream tools [CW-2247]
  sort -k 1,1 -k2,2n human_GRCh38_no_alt_analysis_set.trf.bed |             bedtools merge -i - |             bedtools makewindows -b - -w 25000 > cut.bed
  # Run mosdepth
  mosdepth         -x         -t 2         -b cut.bed         --thresholds 1,10,20,30         --no-per-base         RAD74444381         RAD74444381.cram

Command exit status:
  127

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
  .command.sh: line 8: bedtools: command not found
  .command.sh: line 8: bedtools: command not found

Work dir:
  /scratch/groups/greicius/RUSH_AD/nextflow/RAD74444381_kw/workspace/71/747346622176cf661c72ba80e338e0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
WARN: Killing running tasks (2)

Application activity log entry

No response

RenzoTale88 commented 7 months ago

Hi @kleighwill thanks you for using wf-human-variation. Can you please try the following:

  1. update wf-human-variation to the latest version, and retry your analysis: nextflow pull epi2me-labs/wf-human-variation -r 1.9.0
  2. Set the NXF_SINGULARITY_CACHEDIR and SINGULARITY_TMPDIR to a custom directory, where the singularity images will be stored; for instance, looking at your path: 
    mkdir /scratch/groups/greicius/RUSH_AD/nextflow/.singularity
export NXF_SINGULARITY_CACHEDIR=/scratch/groups/greicius/RUSH_AD/nextflow/.singularity
export SINGULARITY_TMPDIR=/scratch/groups/greicius/RUSH_AD/nextflow/.singularity

    and try the run again.

Andrea

kleighwill commented 7 months ago

Hi Andrea,

It looks like this (and the removal of the bed file in my command) worked for me. Thanks for your help!

Regards,

Kennedy

From: Andrea Talenti @.> Sent: Monday, November 20, 2023 2:01 AM To: epi2me-labs/wf-human-variation @.> Cc: Kennedy Williams @.>; Mention @.> Subject: Re: [epi2me-labs/wf-human-variation] The --snp workflow is halted due to a mosdepth/bedtools error: "command not found" (Issue #116)

Hi @kleighwillhttps://github.com/kleighwill thanks you for using wf-human-variation. Can you please try the following:

  1. update wf-human-variation to the latest version, and retry your analysis: nextflow pull epi2me-labs/wf-human-variation -r 1.9.0
  2. Set the NXF_SINGULARITY_CACHEDIR and SINGULARITY_TMPDIR to a custom directory, where the singularity images will be stored; for instance, looking at your path:

mkdir /scratch/groups/greicius/RUSH_AD/nextflow/.singularity export NXF_SINGULARITY_CACHEDIR=/scratch/groups/greicius/RUSH_AD/nextflow/.singularity export SINGULARITY_TMPDIR=/scratch/groups/greicius/RUSH_AD/nextflow/.singularity

and try the run again.

Andrea

— Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-human-variation/issues/116#issuecomment-1818729190, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BB5I36HX5UZKIXKYX656F2LYFMS7RAVCNFSM6AAAAAA7QM2EEWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJYG4ZDSMJZGA. You are receiving this because you were mentioned.Message ID: @.***>