test failure

[achristofferson-bbi]

Description of the bug

when the following command is run the test profile fails nextflow run nf-core/methylseq
-profile test,singularity
--outdir /projects/team/bioinformatics/nextflow_testing
--em_seq

Command used and terminal output

nextflow run nf-core/methylseq \
  -profile test,singularity \
  --outdir /projects/team/bioinformatics/nextflow_testing \
  --em_seq

executor >  slurm (18)
[f2/75208c] process > NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION (BismarkIndex/genome.fa) [100%] 1 of 1 ✔
[4b/d327e9] process > NFCORE_METHYLSEQ:METHYLSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)              [100%] 1 of 1 ✔
[1d/0ff225] process > NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ (SRR389222_sub2)                                        [100%] 1 of 1 ✔
[42/8765e1] process > NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (SRR389222_sub2)                                           [100%] 3 of 3 ✔
[02/e5d1b7] process > NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (SRR389222_sub2)                                       [100%] 3 of 3 ✔
[be/805c6f] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (SRR389222_sub2)                            [100%] 3 of 3 ✔
[b6/996758] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:SAMTOOLS_SORT_ALIGNED (SRR389222_sub2)                    [100%] 3 of 3 ✔
[da/c0e0ca] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub2)                      [100%] 3 of 3, failed: 2 ✘
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_METHYLATIONEXTRACTOR                              -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_REPORT                                            -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_SUMMARY                                           -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:SAMTOOLS_SORT_DEDUPLICATED                                -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:QUALIMAP_BAMQC                                                    -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:PRESEQ_LCEXTRAP                                                   -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                       -
[-        ] process > NFCORE_METHYLSEQ:METHYLSEQ:MULTIQC                                                           -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/methylseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub1)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE (SRR389222_sub1)` terminated with an error exit status (255)

Command executed:

  deduplicate_bismark \
       \
      -s \
      --bam SRR389222_sub1_trimmed_bismark_bt2.bam

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_DEDUPLICATE":
      bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  Processing single-end Bismark output file(s) (SAM format):
  SRR389222_sub1_trimmed_bismark_bt2.bam


  If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

  Checking file >>SRR389222_sub1_trimmed_bismark_bt2.bam<< for signs of file truncation...

  ### File appears to be empty, terminating deduplication process. Please make sure the input file has not been truncated. ###

Work dir:
  /projects/team/bioinformatics/nextflow_testing/work/b9/16a4f7d01afeea098756cd8c70a175

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