Entering edit mode
6.5 years ago
windsur
▴
20
Dear all,
I have changed the work station and now I am using Centos 7 as operating system.
And if I write this I found that I think I do not have such memory as run a pipeline (in python) to analyse an exome-seq
> free -h
total used free shared buff/cache available
Mem: 7,5G 1,9G 665M 435M 5,0G 4,9G
Swap: 1,9G 1,1G 816M
I've tried with a little sample but when I start mapping the fastq files (using BWA), I reach that:
---------------------------------------------------------------------------------------
Mapping fastq files (BWA)
---------------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bwa_idx2mem] Failed to allocate 4705743064 bytes at bwa.c line 346: Cannot allocate memory
So my question is how much memory do you recommend me to have, or if there is another way.
thanks!
P.s. I am talking about human samples, using hg19 as genome ref.
You are really close to the memory limit with your 5G available to map reads against human genome using BWA. What are your command lines to index your reference genome and to align your reads ?
You can take a look to HISAT which has AFAIK the lowest memory requirement.
Thanks! I will try to add more memory and also what you said.
what I use is:
after that I take the sam file and using samtools I create the sorted bam file:
Did you successfully index your
genome_ref
?In your python code try to print your
call
command and copy/paste them here, it's really hard to investigate with all these variablesFor exome sequencing, better stay with BWA mem, as it is the standard aligner for many downstream tools, including most variant and SV callers.
True, that was just a memory test first, and if OP has no other choice HISAT would have be one solution
Thanks Bastian, I will try with HISAT too. And to index my reference I have followed the steps of GATK
The question about your index was, was it sucessfull ?
hey Bastian, yes it was sucessfull
Exactly! after using samtools I unload the genome reference:
Or should I not use samtools for the analysis you mean?