Hi everyone! I've seen someone in the past encount...
# fetchngs
r
Hi everyone! I've seen someone in the past encountered a similar problem but with a different status exit (alas I did not find any help in previous threads)... I'm trying to download a few - big - fastqs but the pipeline fails just after the annotation retrieval without even starting the actual fastq files download. The command triggering the error (as per nextflow report) is the following:
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curl \
      --retry 5 --continue-at - --max-time 120000 \
      -L ftp.sra.ebi.ac.uk/vol1/fastq/SRR762/000/SRR7621290/SRR7621290_1.fastq.gz \
      -o SRX4451231_SRR7621290_1.fastq.gz
with an exit status 56
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curl: (56) Recv failure: Connection reset by peer
some other times the pipeline fails with an error 7:
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curl: (7) Failed to connect to ftp.sra.ebi.ac.uk port 21 after 6564 ms: Connection refused
But if I run the same command above (curl) without nextflow the download proceeds and completes correctly. In both cases (using nf-core/fetchngs & using SLURM/curl command) I'm using the same parameters. With nextflow the arguments
--retry 5 --continue-at - --max-time 120000
are passed through the config file and the profile used is a
slurm,singularity
(orchestrator and container). No useful (to me at least) additional info in the log files... Anyone any idea on which side the issue could be?