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longphase: command not found #234

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f-ferraro opened this issue Jan 3, 2025 · 3 comments
Closed

longphase: command not found #234

f-ferraro opened this issue Jan 3, 2025 · 3 comments

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@f-ferraro
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f-ferraro commented Jan 3, 2025 •
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Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v2.6.0

Workflow Execution

Other (please describe)

Other workflow execution

Azure batch

EPI2ME Version

No response

CLI command run

sudo nextflow run epi2me-labs/wf-human-variation
--bam 'wf-human-variation-demo/demo.bam'
--ref 'wf-human-variation-demo/demo.fasta'
--bed 'wf-human-variation-demo/demo.bed'
--out_dir 'wf-human-variation-demo/output'
--sample_name 'DEMO'
--snp
--output_xam_fmt bam
-c "/home/adminFede/minimum-wf-hvar.config"
-profile standard

Workflow Execution - CLI Execution Profile

standard

What happened?

Hi,

It seems that the epi2me-labs/wf-human-variation is not able to call longphase after running clair3.

We would be grateful for any pointers!
Best,
Federico

Relevant log output

 N E X T F L O W   ~  version 24.10.3

Launching `https://github.com/epi2me-labs/wf-human-variation` [berserk_lumiere] DSL2 - revision: 036d1ac08c [master]


||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-human-variation v2.6.0-g036d1ac
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : berserk_lumiere
  containerEngine: docker
  container      : [withLabel:wf_human_snp:ontresearch/wf-human-variation-snp:sha17e686336bf6305f9c90b36bc52ff9dd1fa73ee9, withLabel:wf_human_sv:ontresearch/wf-human-variation-sv:shac591518dd32ecc3936666c95ff08f6d7474e9728, withLabel:wf_human_mod:ontresearch/modkit:shaa7bf2b62946eeb7646b9b9d60b892edfc3b3a52c, withLabel:wf_cnv:ontresearch/wf-cnv:sha428cb19e51370020ccf29ec2af4eead44c6a17c2, withLabel:wf_human_str:ontresearch/wf-human-variation-str:shadd2f2963fe39351d4e0d6fa3ca54e1064c6ec057, withLabel:snpeff_annotation:ontresearch/snpeff:shab01c188f11ca9ce53d186fe22111eeac52409523, withLabel:wf_common:ontresearch/wf-common:shaabceef445fb63214073cbf5836fdd33c04be4ac7, withLabel:spectre:ontresearch/spectre:sha42472d37a5a992c3ee27894a23dce5e2fff66d27, default:ontresearch/wf-human-variation:latest]
  launchDir      : REDACTED
  workDir        : /tutorial/work
  projectDir     : /root/.nextflow/assets/epi2me-labs/wf-human-variation
  userName       : root
  profile        : standard
  configFiles    : /root/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config, REDACTED/minimum-wf-hvar.config

Workflow Options
  snp            : true

Main options
  sample_name    : DEMO
  bam            : wf-human-variation-demo/demo.bam
  ref            : wf-human-variation-demo/demo.fasta
  bed            : wf-human-variation-demo/demo.bed
  out_dir        : wf-human-variation-demo/output

Advanced Options
  output_xam_fmt : bam

!! 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 v2.6.0-g036d1ac.
--------------------------------------------------------------------------------
Uploading local `bin` scripts folder to az://tutorial/work/tmp/REDACTED/bin
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
executor >  azurebatch (86)
[97/5032e2] prepare_reference:cram_cache (1)  [100%] 1 of 1 ✔
[07/05bbe1] ingress:checkBamHeaders (1)       [100%] 1 of 1 ✔
[-        ] ingress:sortBam                   -
[-        ] ingress:mergeBams                 -
[-        ] ingress:catSortBams               -
[8b/3bb378] ingress:validateIndex (1)         [100%] 1 of 1 ✔
[-        ] ingress:samtools_index            -
[cc/74d0e9] ingress:check_for_alignment (1)   [100%] 1 of 1 ✔
[b5/49d099] ingress:minimap2_alignment (1)    [100%] 1 of 1 ✔
[8d/d19081] getGenome (1)                     [100%] 1 of 1 ✔
[f7/5cf01e] sanitise_bed (1)                  [100%] 1 of 1 ✔
[a4/bacae8] mosdepth_input (1)                [100%] 1 of 1 ✔
[69/fd9caf] getVersions                       [100%] 1 of 1 ✔
[fe/8048fa] getParams                         [100%] 1 of 1 ✔
[3f/306b64] get_region_coverage (1)           [100%] 1 of 1 ✔
[8c/9b6aea] readStats (1)                     [100%] 1 of 1 ✔
[df/47c4f4] infer_sex (1)                     [100%] 1 of 1 ✔
[2c/af8375] makeAlignmentReport               [100%] 1 of 1 ✔
[-        ] failedQCReport                    -
[c7/40184e] lookup_clair3_model (1)           [100%] 1 of 1 ✔
[d3/9d73c6] snp:make_chunks (1)               [100%] 1 of 1 ✔
[18/4a9094] snp:pileup_variants (48)          [100%] 49 of 49 ✔
[87/62d411] snp:aggregate_pileup_variants (1) [100%] 1 of 1 ✔
[7e/818d32] snp:select_het_snps (3)           [100%] 3 of 3 ✔
[be/7ae176] snp:phase_contig (1)              [100%] 3 of 3, failed: 3 ✘
[14/1fbd6d] snp:get_qual_filter (1)           [100%] 1 of 1 ✔
[dd/ad91d0] snp:create_candidates (3)         [100%] 3 of 3 ✔
[-        ] snp:evaluate_candidates           -
[-        ] snp:aggregate_full_align_variants -
[-        ] snp:merge_pileup_and_full_vars    -
[-        ] snp:aggregate_all_variants        -
[-        ] bed_filter                        -
[-        ] annotate_snp_vcf                  -
[-        ] concat_snp_vcfs                   -
[-        ] sift_clinvar_snp_vcf              -
[-        ] vcfStats                          -
[35/0e5934] report_snp:getVersions            [100%] 1 of 1 ✔
[3a/60daf5] report_snp:getParams              [100%] 1 of 1 ✔
[-        ] report_snp:makeReport             -
[-        ] output_snp                        -
[-        ] combine_metrics_json              [  0%] 0 of 1
[e5/d0197e] publish_artifact (8)              [100%] 8 of 8 ✔
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'snp:phase_contig (1)'

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


Command executed:

  echo "Using longphase for phasing"
  longphase phase --ont -o phased_chr6             -s chr6.vcf.gz -b DEMO.bam -r demo.fasta -t 4
  bgzip phased_chr6.vcf
  tabix -f -p vcf phased_chr6.vcf.gz

Command exit status:
  127

Command output:
  Using longphase for phasing

Command error:
  .command.sh: line 3: longphase: command not found

Work dir:
  az://tutorial/work/be/REDACTED

Container:
  ontresearch/wf-human-variation:latest

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

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response
@f-ferraro f-ferraro changed the title Azure: mosdepth command not found longphase: command not found Jan 8, 2025
@swartpc
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swartpc commented Feb 10, 2025

I'm encountering the same issue.

@SamStudio8
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Container:
  ontresearch/wf-human-variation:latest

You appear to have changed the container configurations which is unsupported. We do not use latest version tags in our workflows as latest is not guaranteed to give the same image across time.

@SamStudio8
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@swartpc Please open a new issue following the Bug Report template if you're suffering this issue without using latest.

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@SamStudio8 @swartpc @f-ferraro