Hera from Bioconda crashes on me

[holtgrewe]

I'm using v1.0.1 from Bioconda and the GRCh38 downloaded index with hs38.fa.

I'm putting the RNA-seq from here into Hera: https://www.encodeproject.org/experiments/ENCSR001UXR/

Am I doing anything wrong? Does this work for you?

Edit: The ticket was a crash because of missing file names on the command line. However, Hera crashes on me regardlessly of what I do.

[GinnyAquarius]

hi holtgrewe, Can you give us more detail about your command? We have run hera on your sample ENCLB020LQS and it work well for both transcriptome:

./build/hera quant -i index38 -t 32 ENCFF386MOY.fastq.gz ENCFF541KUW.fastq.gz 
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact info@bioturing.com if you need further support
Process paired-end reads in:
     1. ENCFF386MOY.fastq.gz
     2. ENCFF541KUW.fastq.gz
Number of aligned pairsr: 19107286/26087337     
Mean read length    : 101.000000
Mean fragment length    : 154.022693
Finish EM with 54 rounds

and transcriptome + genome:

./build/hera quant -i index38 -t 32 -f index38/GRCh38.fa ENCFF386MOY.fastq.gz ENCFF541KUW.fastq.gz 
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact info@bioturing.com if you need further support
Process paired-end reads in:
     1. ENCFF386MOY.fastq.gz
     2. ENCFF541KUW.fastq.gz
Number of aligned pairsr: 22306580/26087337     
Mean read length    : 101.000000
Mean fragment length    : 155.960055
Finish EM with 53 rounds

or could you pull latest code from hera repository and check if it can work?

Thank you, BioTuring Algorithm Team

[holtgrewe]

Hi, the problem was because I did not reserve enough memory on our SGE cluster system.

[kspham]

Holtgrewe, how much memory do you have on the machine?

[holtgrewe]

The machine has 160GB but I put a too low limit on vmem (the job is then limited by ulimit -v). With increased limit it works now.