search

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
44 stars 16 forks source link

Time LIMIT failure for cases with high amount sequencing reads #314

Closed keyvanelhami closed 4 years ago

keyvanelhami commented 4 years ago

BALSAMIC version balsamic --version balsamic, version 4.2.4

References and other implementations Several cases with high amount of sequencing reads fails on InDelRealigner: Slurm Job_id=414251 Name=BALSAMIC.honestcollie.IndelRealigner.75.sh Failed, Run time 07:00:11, TIMEOUT, ExitCode 0

Below are the cases and the amount of reads for each case:

exoticpiglet - 155 M r-p honestcollie - 170 M r-p pickedelk - 125 M r-p selectewe - 106 M r-p validcrane - 91 M r-p valuedjaguar - 75 M r-p rightjaguar - 85 M r-p epicstag - 180 M r-p moredoe (T/N) - 62 and 50 M r-p mightytahr (T/N) - 55 and 72 M r-p

keyvanelhami commented 4 years ago

@hassanfa I have now updated all samples analyzed this week and failed on indel realigner

hassanfa commented 4 years ago

A quick fix would be to increase indelrealigner time in /home/proj/production/cancer/BALSAMIC/BALSAMIC/config/cluster.json it is line 18, and it is 07:00:00 hours right now if they are urgent:

    "IndelRealigner": {
        "time": "07:00:00",
        "n": 10
    },

Change the time value to "10:00:00", make sure it is quoted and follows the same format. If it works, then we push "10:00:00" hour to master branch.