Entering edit mode
4 months ago
n_navy
•
0
Hello, I tried to generate ref index using STAR with this code;
#!/bin/bash
/truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16
--runMode genomeGenerate
--genomeSAsparseD 2
--limitGenomeGenerateRAM 20000000000
--genomeDir /truba/home/user/index
--genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
--sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf
--genomeSAindexNbases 12_*
But it gave error;
*-bash-4.2$ ./generate_index.sh
Apr 17 10:17:17 ..... started STAR run
Apr 17 10:17:17 ... starting to generate Genome files
Apr 17 10:21:17 ..... processing annotations GTF
Apr 17 10:21:48 ... starting to sort Suffix Array. This may take a long time...
Apr 17 10:22:00 ... sorting Suffix Array chunks and saving them to disk...
./generate_index.sh: line 11: 73189 CPU time limit exceeded (core dumped) /truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16 --runMode genomeGenerate --genomeSAsparseD 2 --limitGenomeGenerateRAM 20000000000 --genomeDir /truba/home/user/index --genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf --genomeSAindexNbases 12*
**And ref is not completed;**
*Log.out chrName.txt chrStart.txt exonInfo.tab sjdbList.fromGTF.out.tab
chrLength.txt chrNameLength.txt exonGeTrInfo.tab geneInfo.tab transcriptInfo.tab*
What should I do?
Thanks.
I add these parameters;
But it keeps giving error
You're allocating 4 compute nodes (
#SBATCH -N 4
), but STAR can't actually make use of more than 1 compute node. You can increase the number of cores you're using on a single node, however ,by changing the value given to#SBATCH -c
. 10 or 12 cores should be sufficient to build the index in a couple of hours or so, but be sure to check with your cluster documentation to determine what is allowed and what, if any, costs would be incurred.Please tell us what the error is.
Error is; line 16: 75475 Killed or core dumped.
I increase the core but it did not work. Can you please write the parameters?