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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Sqm run completed but some steps had error #684

Closed aalkin2001 closed 1 year ago

aalkin2001 commented 1 year ago

Hi, I successfully ran all steps for SQM analysis, but unfortunately, there are error messages for steps 14, 15, and 20. I've attached screenshots of error messages and the syslog. I want to know why I encountered an error in these steps.

Thank you.

Step 14 error Step 15 error Step 20 error syslog.zip

fpusan commented 1 year ago

This may be the same problem as your previous issue #683. The binary for jgi_summarize_bam_contig_depths may not work for you due to some binary mismatch. You can try running that command on its own (the first line of your screenshot) to confirm that this is indeed the problem. If so you will need to 1) Download metabat2 from https://bitbucket.org/berkeleylab/metabat/src/master/ 2) Compile 3) Replace the metabat2 and jgi_summarize_bam_contig_depths binaries in /path/to/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin with the ones that you just compiled recompile

aalkin2001 commented 1 year ago

Thank you for getting back to me. After running the script: jgi_summarize_bam_contig_depths, I got the error message below. Does it point to binary mismatch as the problem? Unrecognized character \x7F; marked by <-- HERE after <-- HERE near column 1 at jgi_summarize_bam_contig_depths line 1.

fpusan commented 1 year ago

How did you run it exactly?

aalkin2001 commented 1 year ago

Here it is. perl /gpfs/home/aalafiatayo/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths

fpusan commented 1 year ago

Remove the perl

aalkin2001 commented 1 year ago

This is error message without perl: /gpfs/home/aalafiatayo/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /gpfs/home/aalafiatayo/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths)

fpusan commented 1 year ago

Yeah, then it is rh same problem as before. See my instructions above on how to fix it

El mié., 17 may. 2023 18:56, aalkin2001 @.***> escribió:

This is error message with perl: /gpfs/home/aalafiatayo/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /gpfs/home/aalafiatayo/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/jgi_summarize_bam_contig_depths)

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aalkin2001 commented 1 year ago

Thank you, I will work on it.

fpusan commented 1 year ago

Hope the solution worked. Closing due to lack of activity, feel free to reopen!