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