Cufflinks segfaults on every run

[tavinathanson]

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