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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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qsub issue: file not found #153

Closed rspfau closed 3 years ago

rspfau commented 3 years ago

I'm attempting to run NOVOplasty on a remote computer cluster using a qsub script, but it returns "file not found".

When I have the read files in the same directory as NOVOplasty script, it runs fine. But I need to have the read files in a shared directory. In the config file, I reference the absolute path of the file in the shared directory. I know this path works and the file is there because I can execute "zcat /DAS/sharedData/tarleton/lepus_europaeus_1.gz | head -n 8" from any directory and view the first 8 lines of the read file.

Is this a problem with the computer cluster, NOVOplasty, or my own ignorant error?

The screenshot showing shared directory path, qsub script, config file, the cluster output file are attached.

lepus_novoplasty.qsub.txt test1.o73326.txt config_lepus.txt shared-directory

ndierckx commented 3 years ago

It should not be a problem, I also run it like that so..

If you go to /home/pfau/lepus in the command line, does it work when you enter "cd /DAS/sharedData/tarleton/" ?

ndierckx commented 3 years ago

And your files are not fasta.gz or fastq.gz, it are illumina reads inside the zipped file?

rspfau commented 3 years ago

We identified the problem as being on the computer cluster. Thanks for confirming that NOVOplasty works in this environment. If you're interested in knowing, I am teaching a Genetic Techniques class were students are using NOVOplasty to assemble mitogenomes and then annotate them. We thank your for providing our students an easy entry into genomics and bioinformatics.

ndierckx commented 3 years ago

Ah that's great! :)