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Spurious "File system ftp://...
already exists" errors when staging
#1725
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Could you please provide the |
Here you go. nextflow.log |
Oh !
|
Right! After some retrying it usually assembles all the tasks correctly. Sometimes it does not, though. |
I guess it's race condition while loading that package. |
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Fixed f65296b |
That was quick. Thanks a lot! Looking forward to v20.10 then. |
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Bug report
Expected behavior and actual behavior
Expected: no errors during the staging of files
Actual: in roughly 30% of the cases I get the error with the output below
Steps to reproduce the problem
nextflow run nf-core/proteomicslfq -r dev -profile docker --input https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD001819/sdrf.tsv --database https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata-aws/uniprot_yeast_reviewed_isoforms_ups1_crap.fasta_td.fasta
Program output
Environment
Additional context
I am reading ftp URIs from a csv file and passing them to a subsequent step via
input: path(...)
This is most likely a race condition when creating the file system. I can see the error here:
nextflow/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
Line 78 in 553c311
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