kmtricks crash at merge about kmtricks HOT 2 CLOSED

________________________________ De : Téo Lemane ***@***.***> Envoyé : mardi 26 avril 2022 14:13:52 À : tlemane/kmtricks Cc : Szachnowski Ugo; Author Objet : Re: [tlemane/kmtricks] kmtricks crash at merge (Issue #15) 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<https://docs.oracle.com/cd/E19683-01/816-0210/6m6nb7mo3/index.html>) 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 — Reply to this email directly, view it on GitHub<#15 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AM6YMAFIO3A2VPLGC62R4UTVG7MYBANCNFSM5ULHM5SA>. You are receiving this because you authored the thread.Message ID: ***@***.***>