Open dongspy opened 2 years ago
Changing the bam file into sam file and removing the --readFilesCommand samtools view
, I solved the problem.
Maybe the samtools view took up too much buff/cache.
Hi @lipidong
I suspect that the --readFilesCommand samtools view
may be problematic with the 2-pass mapping option, as the BAM file needs to be read twice. Converting it to SAM first is a good solution.
Cheers Alex
STAR is awesome RNASeq aligner.
I'm running a pipeline that runs the STAR version 2.7.9a , but when trying to mapping with the Human genome(hg38) using the bam file as input on the HPC platform with 32 CPU and 64GB memory, it gets stuck at "inserting junctions into the genome indices" for hours, without generating any errors. And the status of subtask changed to Z(zombie). The indices are created with the same version of STAR.
When I run the same command on the large memory platform with 32 CPU and 128 GB memory, the problem is disappear. For the human genome, is the 64GB memory not enough?
When I run the command using fastq.gz instead of bam as input on the platform with 32 CPU and 64GB memory, the problem is disappear. What is the difference in the way between the two kind of file ?
Below is the detail
code
before running $free -g
running $free -h
Log.out.log