Hi,
I am trying to run abyss with multiple-library pairs. I used this code:
abyss-pe k=96 B=99G name=MYoSEPT lib='p47_405 p47_406 p47_407 p47_408 p87_405 p87_406 p87_407 p87_408'
p47_405='V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz'
p47_406='V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz'
p47_407='V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz'
p47_408='V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz'
p87_405='V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz'
p87_406='V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz'
p87_407='V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz'
p87_408='V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz'
and then when I submitted the job - PBS, 64 cores, 100 Gb, it failed with error:
Running with max stack size of 65536 KB: abyss-bloom-dbg -k96 -q3 -b99G -j64 V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz
bash: line 1: 22670 Killed abyss-stack-size 65536 abyss-bloom-dbg -k96 -q3 -b99G -j64 V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz > MYoSEPT-1.fa
make: *** [/data/common/juanpablo.aguilar/apps/Miniforge3/envs/genomics-forge/bin/abyss-pe.Makefile:555: MYoSEPT-1.fa] Error 137
Any reason why the job failed?
I mapped the reads to the assembly and created a bam file for all the paired libraries. Maybe I should try using the bam files?
Thanks
Hi,
I am trying to run abyss with multiple-library pairs. I used this code:
abyss-pe k=96 B=99G name=MYoSEPT lib='p47_405 p47_406 p47_407 p47_408 p87_405 p87_406 p87_407 p87_408'
p47_405='V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz'
p47_406='V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz'
p47_407='V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz'
p47_408='V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz'
p87_405='V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz'
p87_406='V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz'
p87_407='V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz'
p87_408='V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz'
and then when I submitted the job - PBS, 64 cores, 100 Gb, it failed with error:
Running with max stack size of 65536 KB: abyss-bloom-dbg -k96 -q3 -b99G -j64 V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz
bash: line 1: 22670 Killed abyss-stack-size 65536 abyss-bloom-dbg -k96 -q3 -b99G -j64 V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz > MYoSEPT-1.fa
make: *** [/data/common/juanpablo.aguilar/apps/Miniforge3/envs/genomics-forge/bin/abyss-pe.Makefile:555: MYoSEPT-1.fa] Error 137
Any reason why the job failed?
I mapped the reads to the assembly and created a bam file for all the paired libraries. Maybe I should try using the bam files?
Thanks