Error in rule concatenate_fasta_per_contig: missing fasta file

[JuliusFalck]

I am having trouble getting the GERP part of the pipeline to work. I get this error: a fasta file is missing for one chunk of one of the outgroup species.

This is the Error in the main log:

Error in rule concatenate_fasta_per_contig:

results/logs/13_GERP/genome_chunks/ref_Hirundo_rustica/fasta/chunk38_concatenate_fasta_per_contig.log:

cat: results/gerp/genome_chunks/ref_Hirundo_rustica/fasta/Lagopus_muta_chunk38/Lagopus_muta_NC_053487.1.fasta: No such file or directory

It looks like all the other Fasta chunks have been created except for this one.

My understanding is that the rule bam2fasta should produce the missing file. However, there is no error in that rule log. The only difference with other bam2fasta logs is that the other logs have this line:

[mpileup] 1 samples in 1 input files

right after: Activating singularity image...

But the log for Lagopus_muta chunk38 does not have that line.

Any suggestions for things to try would be very appreciated.

[verku]

Hi Julius!

This part of the pipeline is written in a way so that Snakemake only checks for the presence of the directories holding the files that are produced by the different rules, i.e. Snakemake itself is aware of the folder results/gerp/genome_chunks/ref_Hirundo_rustica/fasta/Lagopus_muta_chunk38/ but not of the file results/gerp/genome_chunks/ref_Hirundo_rustica/fasta/Lagopus_muta_chunk38/Lagopus_muta_NC_053487.1.fasta. As a first test I would therefore suggest that you delete the folder results/gerp/genome_chunks/ref_Hirundo_rustica/fasta/Lagopus_muta_chunk38/ and re-start the pipeline, to see if it was a cluster-related error (which has been in my experience often the case with this type of error). If you still get the same error, let me know!