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nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
https://nf-co.re/circdna
MIT License
25 stars 14 forks source link

Pipeline test is not working #76

Closed yonatans2 closed 1 month ago

yonatans2 commented 1 month ago

Description of the bug

The test profile is not working, appears to need samtools I think

Command used and terminal output

(base) [feshap@n102 ecdna]$ ~/raid/nextflow run nf-core/circdna --outdir ./nf-circ_res/test -profile test
N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/circdna` [special_lalande] DSL2 - revision: 8e0e14c84f [master]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circdna v1.1-g8e0e14c
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : special_lalande
  launchDir                 : /net/mraid14/export/tgdata/users/yonshap/proj/ecdna
  workDir                   : /net/mraid14/export/tgdata/users/yonshap/proj/ecdna/work
  projectDir                : /home/feshap/.nextflow/assets/nf-core/circdna
  userName                  : feshap
  profile                   : test
  configFiles               :

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/circdna/samplesheet/samplesheet.csv
  input_format              : FASTQ
  outdir                    : ./nf-circ_res/test

Circular DNA identifier options
  circle_identifier         : circexplorer2,circle_finder,circle_map_realign,circle_map_repeats,unicycler

Reference genome options
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/circdna/reference/genome.fa
  igenomes_ignore           : true

ampliconarchitect options
  reference_build           : GRCh38

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/circdna for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7712010

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

* Software dependencies
  https://github.com/nf-core/circdna/blob/master/CITATIONS.md

executor >  local (3)
[8a/932aee] process > NFCORE_CIRCDNA:CIRCDNA:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                [100%] 1 of 1 ✔
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CAT_FASTQ                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:FASTQC                                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:TRIMGALORE                                                     -
[8e/b0a417] process > NFCORE_CIRCDNA:CIRCDNA:BWA_INDEX (genome.fa)                                          [  0%] 0 of 1
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BWA_MEM                                                        -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_INDEX_BAM                                             -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                           -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                           -
[d7/61c691] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)                                     [  0%] 0 of 1
executor >  local (3)
[8a/932aee] process > NFCORE_CIRCDNA:CIRCDNA:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                [100%] 1 of 1 ✔
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CAT_FASTQ                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:FASTQC                                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:TRIMGALORE                                                     -
[8e/b0a417] process > NFCORE_CIRCDNA:CIRCDNA:BWA_INDEX (genome.fa)                                          [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BWA_MEM                                                        -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_INDEX_BAM                                             -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                           -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                           -
[d7/61c691] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)                                     [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                -
executor >  local (3)
[8a/932aee] process > NFCORE_CIRCDNA:CIRCDNA:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                [100%] 1 of 1 ✔
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CAT_FASTQ                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:FASTQC                                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:TRIMGALORE                                                     -
[8e/b0a417] process > NFCORE_CIRCDNA:CIRCDNA:BWA_INDEX (genome.fa)                                          [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BWA_MEM                                                        -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_INDEX_BAM                                             -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                           -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                           -
[d7/61c691] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)                                     [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX                       -
executor >  local (3)
[8a/932aee] process > NFCORE_CIRCDNA:CIRCDNA:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                [100%] 1 of 1 ✔
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CAT_FASTQ                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:FASTQC                                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:TRIMGALORE                                                     -
[8e/b0a417] process > NFCORE_CIRCDNA:CIRCDNA:BWA_INDEX (genome.fa)                                          [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BWA_MEM                                                        -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_INDEX_BAM                                             -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                           -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                           -
[d7/61c691] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)                                     [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_SORT_QNAME_CF                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMBLASTER                                                     -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BEDTOOLS_SPLITBAM2BED                                          -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:BEDTOOLS_SORTEDBAM2BED                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CIRCLEFINDER                                                   -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_SORT_QNAME_CM                                         -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_READEXTRACTOR                                        -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_SORT_RE                                               -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_INDEX_RE                                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REPEATS                                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN                                              -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CIRCEXPLORER2_PARSE                                            -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:UNICYCLER                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:SEQTK_SEQ                                                      -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:GETCIRCULARREADS                                               -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:MINIMAP2_ALIGN                                                 -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:CUSTOM_DUMPSOFTWAREVERSIONS                                    -
[-        ] process > NFCORE_CIRCDNA:CIRCDNA:MULTIQC                                                        -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/circdna] Pipeline completed with errors-
WARN: Access to undefined parameter `enable_conda` -- Initialise it to a default value eg. `params.enable_conda = some_value`
ERROR ~ Error executing process > 'NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)'

Caused by:
  Process `NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX (genome.fa)` terminated with an error exit status (127)

Command executed:

  samtools \
      faidx \
      genome.fa \

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_FAIDX":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

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

Work dir:
  /net/mraid14/export/tgdata/users/yonshap/proj/ecdna/work/d7/61c691844c59c23edbd02b587fc0a8

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

Relevant files

No response

System information

No response

ZabalaAitor commented 1 month ago

Have you tried installing Samtools or using -profile test,docker?

yonatans2 commented 1 month ago

No, I just installed using a conda env and it worked