Error with the __glibc package when installing about pggb HOT 5 CLOSED

Conda's dependencies are always a hell. @piosierra (I am tagging you here in case you know how to fix the problem) had dependency problems, and he solved them by using:

conda install -c bioconda -c conda-forge pggb

Could you please try this way?

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Hi @AndreaGuarracino,

Thanks a lot it worked perfectly using the -c conda-forge. Now, in the meantime I looked both at the GitHub page and at the documentation for pggb, and I have a few questions:

1. I will assemble a diploid pangenome for five human individuals, in order to merge the .fasta files can I simply use cat?
2. I had a look at the — suggested settings for different organisms section — and at the — Organism Example Parameters section — in both there is a -G flag that even after looking into the help file of the tool I couldn't really relate to anything I know. It seems to be some sort of threshold for smoothing over particular features of the graph based on their size? Am I correct, if not what is it and how should I use it?
3. After the merging is done, I will index my input.fa with samtools faidx; however, having to deal with only 10 haplotypes in total is it worth to go for PanSN prefix naming pattern? I'm more than happy to do so if this will become a standard and if in any way can make the VGS more organised, I was just wondering whether it would require additional pre-processing

Thanks again, for now I think these are my main doubts. Sorry for the long message, but I also have limited CPU hours on the cluster I'm using, so I want to be sure to maximize the results at each step.

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Yes, you can simply use cat to merge the files. This should be done at the same time as you assign unique names to all the contigs. PanSN is a consistent way to do this that plays well with tools that require sample and haplotype grouping information. IMO, this pattern (one FASTA input for the whole pangenome) isn't ideal but it is organized and avoids later confusion. It also lets you do things like map reads or contigs against the entire pangenome with wfmash. I'd suggest using bgzip and samtools faidx to index the concatenated FASTA file. It does make sense to be organized even with 5 genomes.

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@ekg thanks a lot. I'm not familiar with awk as indicated on PanSN-spec, so I was wondering is there a way consistently name individuals' .fasta with fastix? I had a look at the Git page but couldn't find any indication on how to use it... Is it just a little script that does the job for you? Let me know, thanks.

FYI, this is a tree -h output of the folder where I'm working:

Maybe it is helpful for you to suggest me how to proceed, thanks again.

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We solved the problem privately, but for future possible readers, here is a link with an example about how to rename the sequences by following the PanSN-spec convention and using fastix.

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