Issue in RNA seq pipeline

[Varda06]

Description of the bug

executor > local (4)
[21/7dc9bc] NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (hg38.knownGene.gtf.gz) [100%] 1 of 1, cached: 1 ✔
[fc/771f1f] NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (hg38.fa) [100%] 1 of 1, cached: 1 ✔
[e4/fcb90c] NFCORE_RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/hg38.fa) [100%] 1 of 1, cached: 1 ✔
[15/ca2df1] NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (hg38.fa) [100%] 1 of 1, cached: 1 ✔
[4c/01ed3f] NFCORE_RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES (hg38.filtered.gtf) [100%] 1 of 1, cached: 1 ✔
[a4/bf9864] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (ctrl1) [100%] 4 of 4, cached: 4 ✔
[06/225ceb] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (ctrl2) [100%] 4 of 4, cached: 4 ✔
[97/de67c8] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (US2) [100%] 4 of 4, cached: 4 ✔
[09/98c263] NFC…E_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (US1) [100%] 4 of 4, cached: 4 ✔
[a3/756dad] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (ctrl1) [100%] 4 of 4, cached: 4 ✔
[1b/fa77c4] NFC…EQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1, cached: 1 ✔
[8e/30b2be] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (ctrl1) [100%] 4 of 4, cached: 4 ✔
[3e/d79a51] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (ctrl1) [100%] 4 of 4, cached: 4 ✔
[94/c45244] NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (ctrl1) [100%] 4 of 4, cached: 4 ✔
[9d/409252] NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (ctrl1) [100%] 4 of 4, cached: 4 ✔
[6a/b1417f] NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (ctrl1) [100%] 4 of 4, cached: 4 ✔
[97/4bbd8b] NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (US2) [100%] 4 of 4, cached: 4 ✔
[df/7052bb] NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (US2) [100%] 4 of 4, cached: 4 ✔
[08/01b109] NFC…_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (ctrl2) [100%] 4 of 4, cached: 4 ✔
[07/2cf281] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (ctrl1) [100%] 4 of 4, failed: 4 ✘
[- ] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX -
[- ] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -
[- ] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE -
[- ] NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS -
[- ] NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE -
[- ] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW -
[- ] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV -
[- ] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP -
[- ] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG -
[- ] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP -
Plus 11 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnaseq] Pipeline completed with errors-
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Biotype attribute 'gene_biotype' not found in the last column of the GTF file!

Biotype QC will be skipped to circumvent the issue below:
#460

Amend '--featurecounts_group_type' to change this behaviour.

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (US2)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (US2)` terminated with an error exit status (255)


Command executed:

  picard \
      -Xmx81920M \
      MarkDuplicates \
      --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp \
      --INPUT US2.sorted.bam \
      --OUTPUT US2.markdup.sorted.bam \
      --REFERENCE_SEQUENCE hg38.fa \
      --METRICS_FILE US2.markdup.sorted.MarkDuplicates.metrics.txt                    
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES":
      picard: $(echo $(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Terminating squashfuse_ll after timeout
  INFO:    Timeouts can be caused by a running background process
  FATAL:   container creation failed: while applying cgroups config: rootless cgroups require a D-Bus session - check that XDG_RUNTIME_DIR and DBUS_SESSION_BUS_ADDRESS are set

Work dir:
  /wynton/group/ahituv/bin/pipelines/nf-core-rnaseq/work/1c/322b15a025716d66c53f00c1db9d2f

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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







### Command used and terminal output

```console
I am not sure what needs to be done here
```

### Relevant files

_No response_

### System information

_No response_