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Premature EOF #102

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mvheetve opened this issue Jan 28, 2025 · 1 comment
Closed

Premature EOF #102

mvheetve opened this issue Jan 28, 2025 · 1 comment
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@mvheetve
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Description of the bug

Hi there,

I tried running bamtofastq for the first time but I'm having trouble fetching the repo it seems. Log file provided, from a job submitted on a SLURM cluster, which throws the error Premature EOF. Tried fetching manually, on the same hpc environment, withgit clone and got the following output:

$ git clone https://github.com/nf-core/bamtofastq.git
Cloning into 'bamtofastq'...
remote: Enumerating objects: 3942, done.
remote: Counting objects: 100% (448/448), done.
remote: Compressing objects: 100% (161/161), done.
error: RPC failed; curl 18 transfer closed with outstanding read data remaining
error: 5431 bytes of body are still expected
fetch-pack: unexpected disconnect while reading sideband packet
fatal: early EOF
fatal: fetch-pack: invalid index-pack output

A quick try locally did not encounter the same error, but rather the expected errors associated with pipeline validation:

nextflow run nf-core/bamtofastq -r 2.1.1 
Nextflow 24.10.4 is available - Please consider updating your version to it
N E X T F L O W  ~  version 23.10.1
Pulling nf-core/bamtofastq ...
 downloaded from https://github.com/nf-core/bamtofastq.git
Launching `https://github.com/nf-core/bamtofastq` [extravagant_coulomb] DSL2 - revision: 38fdb8beca [2.1.1]
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bamtofastq v2.1.1-g38fdb8b
------------------------------------------------------
Core Nextflow options
  revision   : 2.1.1
  runName    : extravagant_coulomb
  launchDir  : /Users/mvheetve
  workDir    : /Users/mvheetve/work
  projectDir : /Users/mvheetve/.nextflow/assets/nf-core/bamtofastq
  userName   : mvheetve
  profile    : standard
  configFiles: 

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

* The pipeline
  https://doi.org/10.5281/zenodo.4710628

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

* Software dependencies
  https://github.com/nf-core/bamtofastq/blob/master/CITATIONS.md
------------------------------------------------------
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter: --input
* Missing required parameter: --outdir

 -- Check script '.nextflow/assets/nf-core/bamtofastq/./workflows/../subworkflows/local/utils_nfcore_bamtofastq_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf' at line: 57 or see '.nextflow.log' file for more details

Neither me or my colleagues have ever encountered such an issue. Would love to hear your thoughts on this.

Regards
Mattias

Command used and terminal output

/kyukon/data/gent/vo/000/gvo00082/vsc43079/software/miniforge3/bin/nextflow \
-log ${OUTDIR}/.nextflow.log \
run nf-core/bamtofastq \
-r 2.1.1 \
-resume \
-latest \
-profile vsc_ugent \
-work-dir ${WORKDIR} \
--input ${samplesheet} \
--fasta ${fasta} \
--fasta_fai ${fai} \
--multiqc_title nf-convert_cramtofastq_CMT \
--outdir ${OUTDIR}

Relevant files

.nextflow.log

System information

N E X T F L O W ~ version 24.10.3
HPC
SLURM
Singularity
RHEL9
bamtofastq v2.1.1

@mvheetve mvheetve added the bug Something isn't working label Jan 28, 2025
@mvheetve
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git config --global core.compression 9 before running the nextflow command solved the issue for me as per StackOverflow.

Still not sure what happens here, but the thread speaks of a memory issue.

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