Comments (2)
Hello,
Sorry for this issue. It seems that the maximum number of simultaneously opened files has been reached on your system. Since you have a large number of samples, kmtricks needs to open a lot of files during the merge.
You can try to increase this limit (see ulimit) and/or reduce the number of threads.
To avoid recomputing the first steps during your tests, I suggest to split the pipeline as follows:
1/ Count
kmtricks pipeline --file list_fastq_kmtricks --run-dir kmtricksDir --kmer-size 31 --hard-min 5 --mode kmer:count:bin --until count --cpr -t 12
2/ Merge
kmtricks merge --run-dir kmtricksDir --recurrence-min 10 --mode kmer:count:bin --cpr -t <nb_threads>
This way you can do several merge tries without recounting the partitions.
I hope this help.
Téo
from kmtricks.
from kmtricks.
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