Salmon quant crashed

[alexg9010]

Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v0.9.1
### [ program ] => salmon
### [ command ] => quant
### [ index ] => { /scratch/AG_Akalin/agosdsc/projects/andreas_rnaseq/analysis/salmon_index }
### [ libType ] => { A }
### [ threads ] => { 8 }
### [ mates1 ] => { /scratch/AG_Akalin/agosdsc/projects/andreas_rnaseq/analysis/trimmed_reads/N2_1_R1.fastq.gz }
### [ mates2 ] => { /scratch/AG_Akalin/agosdsc/projects/andreas_rnaseq/analysis/trimmed_reads/N2_1_R2.fastq.gz }
### [ output ] => { /scratch/AG_Akalin/agosdsc/projects/andreas_rnaseq/analysis/salmon_output/N2_1 }
### [ seqBias ] => { }
### [ gcBias ] => { }
### [ geneMap ] => { /data/akalin/Base/Annotation/ce11/ENSEMBL91/Caenorhabditis_elegans.WBcel235.91.gtf }
Logs will be written to /scratch/AG_Akalin/agosdsc/projects/andreas_rnaseq/analysis/salmon_output/N2_1/logs
[2018-03-08 12:22:45.723] [jointLog] [info] parsing read library format
[2018-03-08 12:22:45.723] [jointLog] [info] There is 1 library.
[2018-03-08 12:22:45.761] [jointLog] [info] Loading Quasi index
[2018-03-08 12:22:45.762] [jointLog] [info] Loading 32-bit quasi index
[2018-03-08 12:22:45.762] [stderrLog] [info] Loading Suffix Array
[2018-03-08 12:22:49.571] [stderrLog] [info] Loading Transcript Info
[2018-03-08 12:22:52.312] [stderrLog] [info] Loading Rank-Select Bit Array
[2018-03-08 12:22:52.417] [stderrLog] [info] There were 35448 set bits in the bit array
[2018-03-08 12:22:52.421] [stderrLog] [info] Computing transcript lengths
[2018-03-08 12:22:52.421] [stderrLog] [info] Waiting to finish loading hash
[2018-03-08 12:22:52.422] [stderrLog] [info] Done loading index
[2018-03-08 12:22:52.422] [jointLog] [info] done
[2018-03-08 12:22:52.422] [jointLog] [info] Index contained 35448 targets

terminate called after throwing an instance of 'std::length_error'
  what():  vector::reserve

Some more information:

These are my samples:

-rw-r--r-- 1 agosdsc AG_Akalin 746M Mar  7 15:52 AO_BT_018_S13_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 743M Mar  7 15:52 AO_BT_018_S13_L003_R2_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 715M Mar  7 15:53 AO_BT_019_S14_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 801M Mar  7 15:53 AO_BT_019_S14_L003_R2_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 819M Mar  7 15:53 AO_BT_020_S15_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 886M Mar  7 15:53 AO_BT_020_S15_L003_R2_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 730M Mar  7 15:53 AO_BT_021_S16_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 781M Mar  7 15:54 AO_BT_021_S16_L003_R2_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 856M Mar  7 15:54 AO_BT_022_S17_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 964M Mar  7 15:54 AO_BT_022_S17_L003_R2_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 893M Mar  7 15:54 AO_BT_023_S18_L003_R1_001.fastq.gz
-rw-r--r-- 1 agosdsc AG_Akalin 989M Mar  7 15:54 AO_BT_023_S18_L003_R2_001.fastq.gz

I requested 20G of memory, but it only used 15G, so that should not be the problem.

[borauyar]

salmon quant crashed

[rekado]

@alexg9010 Is this still a problem in the current version?

[alexg9010]

For my data I still was not able to get it running on neither beast nor the cluster. I was in contact with the developer, but he said for him it worked. I provided him some files for debugging but got no news for now.

[borauyar]

Updating the guix variant of salmon to /gnu/store/pin4wvv0ga5jr1974v99kf47akalc6l4-salmon-0.9.1/bin/salmon fixed the issue.