the fatal error: failed to allocate 16 groups

[YIXIN LI]

I build an Hg19 index and try to run salmon. And when I run salmon0.8.1, I got this kind of error.

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) v0.8.1

### [ program ] => salmon

### [ command ] => quant

### [ index ] => { /work/s174790/gtf_to_fa/hg19_salmon/hg19_index }

### [ libType ] => { A }

### [ mates1 ] => { SRR1636809_1.fastq.gz }

### [ mates2 ] => { SRR1636809_2.fastq.gz }

### [ output ] => { SRR1636809_second_quant }

Logs will be written to SRR1636809_second_quant/logs

ESC[1m[2017-03-13 17:33:56.005] [jointLog] [info] parsing read library format

ESC[00mESC[1m[2017-03-13 17:33:56.005] [jointLog] [info] There is 1 library.

ESC[00mESC[1m[2017-03-13 17:33:56.221] [stderrLog] [info] Loading Suffix Array

ESC[00mESC[1m[2017-03-13 17:33:56.219] [jointLog] [info] Loading Quasi index

ESC[00mESC[1m[2017-03-13 17:33:56.220] [jointLog] [info] Loading 32-bit quasi index

ESC[00msparsehash FATAL ERROR: failed to allocate 16 groups

Any ideas to solve this problems?

[Toby]

Hi,

I was receiving this same error message, and I solved it by allocating more memory to my job when submitting it to our compute cluster. I requested 8G of memory (via 8x1G parallel processes) and it then ran fine.

Hope this helps!