Error opening HMM files for writing

[14zac2]

Hi there,

Sorry to bother you with another issue. I know you have mentioned this code is not being maintained.

I just ran into an errors at step 2.6, where the following error is repeated hundreds of times (but for different individual files):

Error: Failed to open HMM file ortho_output/working/orthogroups/hmm/OG0013476.hmm for writing and

Alignment input open failed.
   couldn't open ortho_output_mikado_backup/working/orthogroups/alignments/OG0008511_NucAlignment.fasta for reading

This then causes step 2.7 to crash.

I also have a small error earlier up the pipeline - not sure if this would have anything to do with it. It occurs right before step 1.1.

Error: Sorted input specified, but the file - has the following out of order record
NC_000002.12    BestRefSeq      CDS     41608   46385   .       -       2       transcript_id "rna-NM_001077710.3"; gene_id "gene-FAM110C"; gene_name "FAM110C";
sort: write failed: 'standard output': Broken pipe
sort: write error
Error: Sorted input specified, but the file - has the following out of order record
NC_000072.7     BestRefSeq      CDS     3372520 3377259 .       -       0       transcript_id "rna-NM_010156.3"; gene_id "gene-Samd9l"; gene_name "Samd9l";
sort: write failed: 'standard output': Broken pipe
sort: write error

I also believe that step 2.5 is supposed to create alignment files with the suffix _NucAlignment.fasta although such files to not exist in my orthogroups/alignments directory (but _ProteinAlignment.fasta files do exist). However in step 2.5, I do not see any error messages and it appears that all orthogroups have been processed.

I am not sure how to fix this issue - do you have any ideas? I am currently trying to dig through the code to figure out what the individual functions are doing. I am also hoping that OrthoFiller has checkpoints that will allow the run to continue at step 2.6 because it has already been running for just over a week. I'm not sure if this is the case, and I'm worried about testing this out in case I overwrite any part of the pipeline. Do you know if this is a default response of OrthoFiller if the same arguments are specified on the command line?

Thanks so much, Zoe

[14zac2]

After a bit more digging, I just found out that OrthoFiller crashed not because of the errors above, but because the number of small files created exceeded my disc quota. Have future versions of OrthoFiller (on your GitLab space) changed in this regard?

Thanks again, Zoe

[14zac2]

Hi - since posting this issue, I have moved to your GitLab version of the code where I realized that much of my problem was due to unwritable Augustus directories which I have since corrected. Working with the new code now, so I will close the issue here.