Bin issue with metabat2

[XC-Zhai]

Thanks for this nice pipeline with conda env, I had an issue when I run SqueezeMeta v1.6.2, where there are missing library (/lib64/libstdc++.so.6). The test_install.pl didn't give me any error.

I am using: NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

It would be great to guide me how to solve this Thanks in advance.

syslog.zip

[fpusan]

Hi! CentOS7 is no longer oficially supported since v1.6.2, since some of it's system libraries are too old. A possible fix would be to run mamba install -c anaconda libstdcxx-ng inside the SqueezeMeta environment. Alternatively, you can recompile metabat2 and jgi_summarize_bam_contig_depths as described in #684

[XC-Zhai]

Hi! CentOS7 is no longer oficially supported since v1.6.2, since some of it's system libraries are too old. A possible fix would be to run mamba install -c anaconda libstdcxx-ng inside the SqueezeMeta environment. Alternatively, you can recompile metabat2 and jgi_summarize_bam_contig_depths as described in #684

Thanks a lot. We are having metabat2 installed at our cluster for anyone to use by using "module load metabat/2.12.1", I am wondering if I can make a link to this and rerun from step14? Or I can run this separately and restart from next step?

Best, Xichuan

[fpusan]

It may work. What I would do then would be to copy the metabat2 and jgi_summarize_bam_contig_depths to the /home/projects/cu_10168/people/xiczha/SqueezeMeta/bin directory. You can locate the scripts with which metabat2 and which jgi_summarize_bam_contig_depths after loading the metabat module.

[XC-Zhai]

It may work. What I would do then would be to copy the metabat2 and jgi_summarize_bam_contig_depths to the /home/projects/cu_10168/people/xiczha/SqueezeMeta/bin directory. You can locate the scripts with which metabat2 and which jgi_summarize_bam_contig_depths after loading the metabat module.

Yes, it worked with the copy-paste method: --restart --force_overwrite for the project already finished from step 14 . And all the further steps could be finished. I had issue with SQM R package, where the data could be loaded and some plot could be generated according to tutorial:https://github.com/jtamames/SqueezeMeta/wiki/Using-R-to-analyze-your-SQM-results.

But I got error when it came to subsetTax: archaea=subsetTax(cow_meta,'superkingdom',tax='Archaea',rescale_copy_number=F) Error in subSQM$bins$tax[bins, , drop = FALSE] : subscript out of bounds

I compared the project from 1st finished and current one and found that there are still something keeping even using --force_overwrite, is this parameter means will remove everything from restart step and write new output? Thanks for your guides.

Best, Xichuan

[XC-Zhai]

It may work. What I would do then would be to copy the metabat2 and jgi_summarize_bam_contig_depths to the /home/projects/cu_10168/people/xiczha/SqueezeMeta/bin directory. You can locate the scripts with which metabat2 and which jgi_summarize_bam_contig_depths after loading the metabat module.

Yes, it worked with the copy-paste method: --restart --force_overwrite for the project already finished from step 14 . And all the further steps could be finished. I had issue with SQM R package, where the data could be loaded and some plot could be generated according to tutorial:https://github.com/jtamames/SqueezeMeta/wiki/Using-R-to-analyze-your-SQM-results.

But I got error when it came to subsetTax: archaea=subsetTax(cow_meta,'superkingdom',tax='Archaea',rescale_copy_number=F) Error in subSQM$bins$tax[bins, , drop = FALSE] : subscript out of bounds

I compared the project from 1st finished and current one and found that there are still something keeping even using --force_overwrite, is this parameter means will remove everything from restart step and write new output? Thanks for your guides.

Best, Xichuan

Seems like I solved it by using #243 .

[fpusan]

Glad to hear everything work out. Closing issue. For reference, as of now --force_overwrite will overwrite results, but not remove the previous ones.