Oma.part2 ** The following file(s) is (are) not yet completed:

[joana-morais]

I’m running oma (part 2) but it doesnt complete (its not a memory problem). The log file indicated:

1736507282.226020 - 1 - [pid 781887]: Pair galba/tiberius_masked part 295 of 414 already computed. Skipped.

** At least 1 process appears to be still computing the all-vs-all.
** The following file(s) is (are) not yet completed:
Cache/AllAll/CalySin_helixer/CROTI/part_878-1089
Cache/AllAll/tiberius_masked/CROTI/part_251-1072
Cache/AllAll/tiberius_masked/CROTI/part_860-1072
Cache/AllAll/tiberius_masked/PYTBI/part_545-679
Cache/AllAll/tiberius_masked/LACAG/part_410-815
Cache/AllAll/galba/PYTBI/part_513-653
Cache/AllAll/galba/CROTI/part_809-1031
Cache/AllAll/galba/CROTI/part_770-1031
Cache/AllAll/galba/CROTI/part_816-1031
Cache/AllAll/galba/CROTI/part_415-1031

** If no other process is running, delete these files and restart.

So there are still files it needs to check but it doesn't. The error file doesn’t show anything. If I delete the files and restart (as it tells me to), I still have the same problem.

Have you ever had this problem and/or know how to fix it?

The command:
`#!/bin/bash
#SBATCH --array=1-500
#SBATCH --partition=begendiv,main
#SBATCH --qos=standard
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=[email protected]
#SBATCH --time=3-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2GB
#SBATCH --job-name=oma2
#SBATCH --export=None
#SBATCH --output=/scratch/joanamorais/jobs/01_OUTandERR/oma_part2.%j.out
#SBATCH --error=/scratch/joanamorais/jobs/01_OUTandERR/oma_part2.%j.err

cd /scratch/joanamorais/jobs/02_Annotation/OMAnnotator/OMA_FOLDER
export NR_PROCESSES=500
./bin/oma -s -W 7000
if [[ "$?" == "99" ]] ; then
scontrol requeue
${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID}
fi
exit 0`

And it works for most of the files, but not all. I already did oma.part1 and the previous steps.