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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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run sqm_hmm_reads.pl error! #619

Closed luozhy88 closed 1 year ago

luozhy88 commented 1 year ago

SqueezeMeta is very good, thank you very much. I have such an error when running this, and I need your help to solve it. image image image

luozhy88 commented 1 year ago
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jtamames commented 1 year ago

Hello I am currently out of the lab with very poor internet connectivity. I will check this asap

jtamames commented 1 year ago

Ok, the problem is that Pfam site (where we were getting the Pfam files) was discontinued and migrated for integration with Interpro. As a quick fix, you can change lines 162 and 166 in sqm_hmm_reads.pl, substituting pfam.xfam.org by pfam-legacy.xfam.org. I will produce a better patch to read interpro instead of Pfam, but that one can work in the meantime. Best, J

luozhy88 commented 1 year ago

Error!! image image

luozhy88 commented 1 year ago

Thanks,it did work. But I have another bug.

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luozhy88 commented 1 year ago
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why?

luozhy88 commented 1 year ago

Can you help me?

luozhy88 commented 1 year ago

Can you help me?

jtamames commented 1 year ago

Did you check if you have writing permissions in the directory where the files are being created? That is, the /data_bk/zhiyu/Project/test/rm_host directory?

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen!