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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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PermanentFail in wget virus #42

Open Samantao93 opened 2 months ago

Samantao93 commented 2 months ago

When I execute this in a Conda environment with all the necessary installations, the human FASTA file downloads successfully. However, when it tries to download the virus FASTA file, it results in a "PermanentFail" error. We are using a proxy, which might be causing the issue. Could you provide guidance on how to resolve this?

createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml

INFO path/.conda/envs/virtus2/bin/cwltool 3.1.20240508115724 INFO Resolved 'path/VIRTUS2/bin/createindex.cwl' to 'file:///path/VIRTUS2/bin/createindex.cwl' INFO [workflow ] start INFO [workflow ] starting step wget_virus INFO [step wget_virus] start INFO [job wget_virus] /tmp/h0_x3dkw$ docker \ run \ -i \ --mount=type=bind,source=/tmp/h0_x3dkw,target=/TkuKdQ \ --mount=type=bind,source=/tmp/r0wueiha,target=/tmp \ --workdir=/TkuKdQ \ --read-only=true \ --user=1012:1012 \ --rm \ --cidfile=/tmp/bes5i9q6/20240812134745-514374.cid \ --env=TMPDIR=/tmp \ --env=HOME=/TkuKdQ \ inutano/wget:1.20.3-r1 \ wget \ --output-document=viruses.fasta \ https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/data/viruses.fasta 2> /tmp/h0_x3dkw/wget-stderr.log INFO [job wget_virus] Max memory used: 0MiB WARNING [job wget_virus] exited with status: 4 WARNING [job wget_virus] completed permanentFail WARNING [step wget_virus] completed permanentFail INFO [workflow ] completed permanentFail { "downloaded_virus": { "location": "file:///path/virtus/results/viruses.fasta", "basename": "viruses.fasta", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "path": "path/virtus/results/viruses.fasta" }, "starIndex_virus": null, "starIndex_human": null, "downloaded_genomefasta_human": null }WARNING Final process status is permanentFail

yyoshiaki commented 2 months ago

Could you see /tmp/h0_x3dkw/wget-stderr.log? wget looks like it is not working.

Samantao93 commented 2 months ago

No, because when it stops doing the wget, it removes the file. I tried, but it happens so fast. Yes, it seems that the issue is with wget, but when I tried using wget with the URL directly, the download completed successfully. I'm not sure why it doesn't work with the createindex.cwl.