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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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can't donwload viral library #221

Closed ALFLAG closed 2 years ago

ALFLAG commented 2 years ago

Hi, when using centrifuge-download, I couldn't download the viral library, while archea and bacteria were OK. Any suggestion ? I used the version 1.0.4, and I installed it using conda.

Thanks in advance. Alex

mperisin-lallemand commented 2 years ago

This appears to be due to the centrifuge-download script line 368: "cut -f "$TAXID_FIELD,$FTP_PATH_FIELD,$FTP_PATH_FIELD2" "$ASSEMBLY_SUMMARY_FILE" | \". I manually changed it to: "cut -f "$TAXID_FIELD,$FTP_PATH_FIELD" "$ASSEMBLY_SUMMARY_FILE" | \", and that solved the issue for me. Further up in that script it on line 305 the FTP_PATH_FIELD2 variable is defined with the following comment, "## Needed for wrongly formatted virus files - hopefully just a temporary fix." So I guess the viral "assembly_summary.txt" has been reformatted so this previously needed fix is no longer necessary.

mourisl commented 2 years ago

I have updated a patch to handle this formatting issue. Thank you for identifying this @mperisin-lallemand !

mwylerCH commented 2 weeks ago

Possible that there is again the same problem?