Unexpected sensitivity to . characters in output name

[DarrenObbard]

On running:

python ~/apps/CenoteTaker2/run_cenote-taker2.py -c $S.scaffolds.fasta --srr_number $S --known_strains blast_knowns --blastn_db /data/BLAST_databases/nt --reads1 $S/$S.trim.1.fq.gz --reads2 $S/$S.trim.2.fq.gz -r $S.virus -m 150 -t 40 -p False

I get a large number of mv and grep errors, when they can't find files, and the final table is empty. If, instead, I choose to run:

python ~/apps/CenoteTaker2/run_cenote-taker2.py -c $S.scaffolds.fasta --srr_number $S --known_strains blast_knowns --blastn_db /data/BLAST_databases/nt --reads1 $S/$S.trim.1.fq.gz --reads2 $S/$S.trim.2.fq.gz -r ${S}_virus -m 150 -t 40 -p False

It completes as expected, albeit with the error:

/data/home/dobbard/apps/CenoteTaker2/cenote-taker2.1.3.sh: line 596: s/#/ /g: No such file or directory

I think the code must have a problem with a '.' in the output file string, which is somewhat unexpected ...

Thanks!

D

[mtisza1]

Hi Darren,

I know it is a hassle to be limited in this way, but, to be fair, it does say right in the command line help menu (and the repo page) under --run_title:

Must be less than 18 characters, using ONLY letters, numbers and underscores (_)

This is a convention that I got locked into with the requirements of tbl2asn. I think I will make the job stop if these requirements are not met so people don't get a bunch of weird errors like that.

Also, just as a side note, I haven't come across a case in my personal use of the tool where it is necessary to use more gigabytes of memory than # of cpus. It might make it easier to schedule jobs on your HPC if you specify fewer gigs of memory.

Best,

Mike

[DarrenObbard]

Sorry! Yes, stop and an error message would solve it.

Any idea why I am getting the "No such file or directory" from line 596? I seem to get as many of these as there are contigs on interest.

I have more Gb of memory than CPUs on my workstation, so there seemed no reason to stint :oD

[mtisza1]

Darren,

I'm aware that it throws the "no such file or directory" error, but rest assured that it does not affect the output otherwise. I'm trying to figure out where the logic is wrong with this piece of code. Just ignore it for now please.

Mike