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Hi, thanks so much for creating and maintaining th...
# atacseq
r
Hi, thanks so much for creating and maintaining the atacseq pipeline, it's very useful. I'm running the dev version on the IFB SLURM cluster (using ifb_core config) and encountering an error that I need help with: [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_ATACSEQATACSEQMERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS (consensus_peaks)' Caused by: Process 
NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS (consensus_peaks)
terminated with an error exit status (1) (...) Command error: INFO: Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred 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 WARNING: While bind mounting '/shared:/shared': destination is already in the mount point list Error: package or namespace load failed for ‘UpSetR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 0.4.12 is being loaded, but >= 1.1.0 is required Execution halted There is no info about the R version loaded by the pipeline in results/nf_core_atacseq_software_mqc_versions.yml although I see 
cat <<-END_VERSIONS > versions.yml
"NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS":
python: $(python --version | sed 's/Python //g')
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
END_VERSIONS
in the command, is this saved in another location? I'd like to know which R version is pulled to update rlang accordingly. I enclose the nextflow.log Thanks in advance
Nevermind, I found the R version from another run using --skip_consensus_peaks. It looks like tools/packages versions are not written in the yml versions file for the MACS3_CONSENSUS steps, cheers
🙌🏻 1
So I reached out to IFB HPC admins and they replied that the pipeline handles the versions of the modules and packages it needs. So it seems that nf-core loads rlang 0.4.12 in r-base: 4.0.3 and is outdated. Could you please look into it? Thanks in advance
s
It looks like you are using apptainer to run the pipeline, so it should be using an appropriate container. Can you share the .command.run from that working directory?
Although I'm a bit confused, because the dev branch doesn't contain 
MACS3_CONSENSUS
as a module under 
MERGED_LIBRARY_CONSENSUS_PEAKS
, it should be 
MACS3_CALLPEAK
So maybe try 
nextflow pull nf-core/atacseq
to ensure you aren't using some really old cached version
r
thanks for the prompt reply, I unfortunately deleted the work and results folders to free some space, from previous runs I found this version info: nf-core/atacseq: v2.2.0dev-gc7b9e7b I will pull the latest version and report back
Checking nf-core/atacseq ... Already-up-to-date - revision: c7b9e7b8f4 [dev]
Hi, I tried again over the weekend (in narrowPeak mode) and ran into the same error:
Copy code
Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS (consensus_peaks)'

Caused by:
  Process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS (consensus_peaks)` terminated with an error exit status (1)
(...)
Copy code
Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred
  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
  WARNING: While bind mounting '/shared:/shared': destination is already in the mount point list
  Error: package or namespace load failed for 'UpSetR' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   namespace 'rlang' 0.4.12 is being loaded, but >= 1.1.0 is required
  Execution halted
attaching the command.run from the wd and the tool versions. As mentioned above, I tried to pull the latest dev version and it was up to date. Thanks in advance
nf_core_atacseq_software_mqc_versions.ymlcommand.run
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