search

nf-core / cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
https://nf-co.re/cutandrun
MIT License
79 stars 45 forks source link

test error with conda #245

Closed lecook closed 3 months ago

lecook commented 3 months ago

Description of the bug

Hello,

I tried running the profile test with conda (nextflow run nf-core/cutandrun -profile test,conda), the job seems to start with no issues but ends with the following error:

ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by: Process NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz) terminated with an error exit status (1)

Thank you!

Command used and terminal output

$ nextflow run nf-core/cutandrun -profile test,conda

Launching `https://github.com/nf-core/cutandrun` [pedantic_bardeen] DSL2 - revision: 6e1125d4fe [master]

WARN: =========================================================================================================
  dt_calc_all_matrix is switched on which will calculate a deeptools matrix for all samples. 
  If you have a large sample count, this may affect pipeline performance and result in errors. 
  Set this option to false to disable this feature and only calculate deeptools heatmaps for single samples
===============================================================================================================

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/cutandrun v3.2.2-g6e1125d
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : pedantic_bardeen
  launchDir                 : /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm
  workDir                   : /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work
  projectDir                : /Users/lbl/.nextflow/assets/nf-core/cutandrun
  userName                  : lbl
  profile                   : test,conda
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv

Reference data options
  bowtie2                   : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
  gene_bed                  : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
  blacklist                 : /Users/lbl/.nextflow/assets/nf-core/cutandrun/assets/blacklists/hg38-blacklist.bed
  spikein_bowtie2           : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
  spikein_fasta             : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz

Pipeline Options
  remove_mitochondrial_reads: true
  mito_name                 : chrM
  remove_linear_duplicates  : true
  macs_gsize                : 2700000000.0
  replicate_threshold       : 1.0

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/cutandrun for your analysis please cite:

  https://doi.org/10.5281/zenodo.5653535

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

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

executor >  local (2)
executor >  local (2)
executor >  local (2)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA                                                 [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF                                                           [  0%] 0 of 1
executor >  local (2)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA                                                 [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF                                                           [  0%] 0 of 1
executor >  local (3)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA                                                 [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [  0%] 0 of 1
executor >  local (3)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA                                                 [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [  0%] 0 of 1
executor >  local (4)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [  0%] 0 of 1
executor >  local (4)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         -
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [  0%] 0 of 1
executor >  local (4)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [  0%] 0 of 1
executor >  local (5)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [  0%] 0 of 1
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
executor >  local (6)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
executor >  local (6)
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA                                                         [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [  0%] 0 of 1
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
Execution cancelled -- Finishing pending tasks before exit
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [  0%] 0 of 1
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
Execution cancelled -- Finishing pending tasks before exit
Creating env using conda: conda-forge::python=3.8.3 conda-forge::pandas=1.3.3 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-ba73a1f2010efb7d86ecdbb8c0ee708b]
Creating env using conda: bioconda::deeptools=3.5.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-0d01150023c68e439ebff3eb959d98bf]
Creating env using conda: conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-1d29d397b4471c4b8cdf778c1da7398c]
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [100%] 1 of 1 ✔
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
Execution cancelled -- Finishing pending tasks before exit
Creating env using conda: conda-forge::python=3.8.3 conda-forge::pandas=1.3.3 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-ba73a1f2010efb7d86ecdbb8c0ee708b]
Creating env using conda: bioconda::deeptools=3.5.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-0d01150023c68e439ebff3eb959d98bf]
Creating env using conda: conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-1d29d397b4471c4b8cdf778c1da7398c]
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [100%] 1 of 1 ✔
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
Execution cancelled -- Finishing pending tasks before exit
Creating env using conda: conda-forge::python=3.8.3 conda-forge::pandas=1.3.3 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-ba73a1f2010efb7d86ecdbb8c0ee708b]
Creating env using conda: bioconda::deeptools=3.5.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-0d01150023c68e439ebff3eb959d98bf]
Creating env using conda: conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-1d29d397b4471c4b8cdf778c1da7398c]
-[nf-core/cutandrun] Pipeline completed with errors-
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
executor >  local (7)
[b9/f95ec9] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_FASTA (hg38-chr20.fa.gz)                                      [100%] 1 of 1 ✔
[1b/bb5b63] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_SPIKEIN_FASTA (e_coli_U00096_3.fa.gz)                         [100%] 1 of 1 ✔
[53/af9daa] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_GTF (hg38-chr20-genes.gtf.gz)                                 [100%] 1 of 1 ✔
[78/905106] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GUNZIP_BED (hg38-chr20-genes.bed.gz)                                 [100%] 1 of 1 ✔
[13/88b819] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT (hg38-chr20-genes)                          [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_TARGET                                                   [  0%] 0 of 1
[d5/4d908f] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT                                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT                                              -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT                                        -
[fa/685f83] process > NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (test-GSE145187-small.csv)                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
[-        ] process > NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS  -
Plus 67 more processes waiting for tasks…
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
Creating env using conda: bioconda::fastqc=0.12.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-49dea791c31ead673ed2e341e1c6d206]
Creating env using conda: bioconda::trim-galore=0.6.6 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-7e075e748f6bfc7634241fa77a653e1e]
Creating env using conda: bioconda::samtools=1.16.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-248d30c220c836f11b9e719864c010e3]
Execution cancelled -- Finishing pending tasks before exit
Creating env using conda: conda-forge::python=3.8.3 conda-forge::pandas=1.3.3 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-ba73a1f2010efb7d86ecdbb8c0ee708b]
Creating env using conda: bioconda::deeptools=3.5.1 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-0d01150023c68e439ebff3eb959d98bf]
Creating env using conda: conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4 [cache /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/conda/env-1d29d397b4471c4b8cdf778c1da7398c]
-[nf-core/cutandrun] Pipeline completed with errors-
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN (e_coli_U00096_3.tar.gz)` terminated with an error exit status (1)

Command executed:

  mkdir e_coli_U00096_3

  ## Ensures --strip-components only applied when top level of tar contents is a directory
  ## If just files or multiple directories, place all in prefix
  if [[ $(tar -taf e_coli_U00096_3.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C e_coli_U00096_3 --strip-components 1 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  else
      tar \
          -C e_coli_U00096_3 \
          -xavf \
           \
          e_coli_U00096_3.tar.gz \
          --no-same-owner
  fi

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_INDEX_SPIKEIN":
      untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  grep: invalid option -- P
  usage: grep [-abcdDEFGHhIiJLlMmnOopqRSsUVvwXxZz] [-A num] [-B num] [-C[num]]
        [-e pattern] [-f file] [--binary-files=value] [--color=when]
        [--context[=num]] [--directories=action] [--label] [--line-buffered]
        [--null] [pattern] [file ...]
  tar: Option -a is not permitted in mode -t
  tar: Option -a is not permitted in mode -x

Work dir:
  /Users/lbl/Library/CloudStorage/GoogleDrive-lecook@lbl.gov/My Drive/collaborations/diaphragm/work/d5/4d908f8171d973e6a49289a85f4eaa

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

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

Relevant files

No response

System information

No response

chris-cheshire commented 3 months ago

hi the pipeline doesnt support conda, please run with a container engine instead