OMA standalone, "-c" to just convert the databases AFTER all vs all

Question

[gusa_10]

After my ALL vs ALL parallelized job (on SLURM), I run OMA 2.1.1 with a single processor and I got this message on multiple lines:

Error, 'unable to ReadProgram(Cache/AllAll/isp1/sp2/part_397-877)' (and some other lines containing another pairwise from AllAll)

I deleted these files (i.e Cache/AllAll/isp1/sp2/part_397-877.gz), launched again the All vs All parallelized job and then OMA as a single processor. Now, I am getting this messages at the end of my job.out:

---

Reading the all-against-all files...

Process 21923 .... 12020: job nr 20 of 20

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Job 20 [pid 21923]: waiting for too long. abort.

It seems that your parallelisation framework hasn't launched the master job properly, or you are using a very slow filesystem. Please restart a single process of OMA with the command line option "-c" to just convert the databases. Once this job successfully finished, you can restart OMA with many parallel jobs.

I do not know what to do at this point, should I run again the data conversion (-c)? If so, Do I need to run again the AllvsAll parallelized job?

Thanks

Answer 1

[Adrian Altenhoff]

Hi Gusa,

unless you changed something on one of the genome files, this should actually not happen (do you find a file Cache/conversion.done) file? Anyways, if you didn't change any input files, then, simply start the single OMA. No need to convert the databases again or run again the parallel mode of the all-against-all. In case a few files are still missing, the process will compute them on the fly. Best wishes Adrian