Open tavinathanson opened 7 years ago
This is on a 32 CPU/208 GB memory machine.
First thing I'll try is running it on a different machine type cc @armish.
Logs:
### Kube-Job 3601de63-2406-5f7d-85ae-44cda16046cf ### Freshness: Fresh ### Output: User biokepi Host 3601de63-2406-5f7d-85ae-44cda16046cf Machine Linux 3601de63-2406-5f7d-85ae-44cda16046cf 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1 (2016-12-30) x86_64 x86_64 x86_64 GNU/Linux biokepi biokepi You are using Cufflinks v2.2.1, which is the most recent release. [23:20:33] Loading reference annotation. [23:25:05] Inspecting reads and determining fragment length distribution. > Processing Locus 1:11868-31109 [ ] 0% > Processing Locus 1:34553-36081 [ ] 0% > Processing Locus 1:52472-54936 [ ] 0% > Processing Locus 1:62947-63887 [ ] 0% > Processing Locus 1:69090-70008 [ ] 0% > Processing Locus 1:89294-134836 [ ] 0% > Processing Locus 1:134900-139379 [ ] 0% > Processing Locus 1:139789-140339 [ ] 0% > Processing Locus 1:141473-173862 [ ] 0% > Processing Locus 1:227614-267253 [ ] 0% > Processing Locus 1:317719-461954 [ ] 0% > Processing Locus 1:470970-471355 [ ] 0% > Processing Locus 1:521368-532878 [ ] 0% > Processing Locus 1:536815-660283 [ ] 0% > Processing Locus 1:661610-663527 [ ] 0% > Processing Locus 1:677192-685396 [ ] 0% > Processing Locus 1:693612-693716 [ ] 0% > Processing Locus 1:694411-714006 [ ] 0% > Processing Locus 1:714149-755214 [ ] 0% > Processing Locus 1:761585-762902 [ ] 0% > Processing Locus 1:762987-794826 [ ] 0% > Processing Locus 1:803450-812283 [ ] 0% > Processing Locus 1:818042-819983 [ ] 0% > Processing Locus 1:840213-851356 [ ] 0% > Processing Locus 1:852244-856396 [ ] 0% > Processing Locus 1:860259-894689 [ ] 0% > Processing Locus 1:895966-901095 [ ] 0% > Processing Locus 1:901876-917497 [ ] 0% > Processing Locus 1:931345-933431 [ ] 0% > Processing Locus 1:934341-935552 [ ] 0% > Processing Locus 1:943455-943609 [ ] 0% > Processing Locus 1:947376-948573 [ ] 0% > Processing Locus 1:948802-949920 [ ] 0% > Processing Locus 1:955502-991496 [ ] 0% > Processing Locus 1:995113-1004735 [ ] 0% [...] > Processing Locus 5:180632360-180633120 [ ] 1% > Processing Locus 5:180649498-180662809 [ ] 1% > Processing Locus 5:180663908-180699308 [ ] 1%/coclo-kube/mount/script: line 94: 38 Segmentation fault cufflinks -p 7 -G /nfs-pool-16/biokepi/reference-genome/b37decoy/transcripts.gtf -o /nfs-pool-16/biokepi/work/results-b37decoy-rna_processing_467/11d44d92f27dc99dc2fbedaa6559b083rna_processing_467b37decoycufflinks-cufflinks_output /nfs-pool-16/biokepi/work/results-b37decoy-rna_processing_467/5507d4dbef1c2d790bdcc08a16367aa5_checkpoint-trials_lung_ipinivo_tumor_bams_AE862349_bamAE862349-sorted.bam
This is on a 32 CPU/208 GB memory machine.
First thing I'll try is running it on a different machine type cc @armish.
Logs: