Sqm run completed but some steps had error

[aalkin2001]

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.

syslog.zip

[fpusan]

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]

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]

How did you run it exactly?

[aalkin2001]

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

[fpusan]

Remove the perl

[aalkin2001]

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]

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) — Reply to this email directly, view it on GitHub <#684 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACAHO7R722R27AUSLXNRNQLXGT7KHANCNFSM6AAAAAAYEBQYGM> . You are receiving this because you commented.Message ID: ***@***.***>

[aalkin2001]

Thank you, I will work on it.

[fpusan]

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