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Originally posted by cindylanzao View PostThanks for your kind reply Alex, I have checked the Log.progress.out, it contains nothing but the title after a whole night's running with only one sample with 12 thread. Do you have any other suggestion? Thanks!
please post or email me the Log.out file from the failed single sample 12-thread run.
Cheers
Alex
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Thanks for your reply
Originally posted by alexdobin View PostHi @cindylanzao
you can check check Log.progress.out for the current mapping speed and progress.
Are you trying to map all 9 samples at the same time with 2 threads for each job? If so, you need to use shared memory option, e.g. --genomeLoad LoadAndKeep. Without shared memory, the genomes for each sample have to be loaded in RAM, which requires ~9*25 GB.
A simpler option would be to map one sample at a time with 12 threads.
Cheers
Alex
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Originally posted by cindylanzao View PostHi,all
I am doing RNA-seq alignment with STAR, my workstation is dual core(E5-2620v3), 12 thread in total, 64G RAM. I am running 9 mouse RNA-seq sample data(1GB/sample), parallelly, two days has gone, still no result. No error, the log just say start mapping. Can any one with similar experience tell me how can I make it faster or is there anything wrong.
Below is my command:
/STAR-STAR_2.4.2a/bin/Linux_x86_64/STAR --outFilterIntronMotifs RemoveNoncanonicalUnannotated --runThreadN 2 --outTmpDir /pathdir/ --outSAMtype BAM SortedByCoordinate --genomeDir /pathfordatabaseformus/ --readFilesIn XXX.clean.fq.gz --readFilesCommand zcat
Thanks for all the guys who offer me help!
you can check check Log.progress.out for the current mapping speed and progress.
Are you trying to map all 9 samples at the same time with 2 threads for each job? If so, you need to use shared memory option, e.g. --genomeLoad LoadAndKeep. Without shared memory, the genomes for each sample have to be loaded in RAM, which requires ~9*25 GB.
A simpler option would be to map one sample at a time with 12 threads.
Cheers
Alex
Leave a comment:
-
Computing time evaluate
Hi,all
I am doing RNA-seq alignment with STAR, my workstation is dual core(E5-2620v3), 12 thread in total, 64G RAM. I am running 9 mouse RNA-seq sample data(1GB/sample), parallelly, two days has gone, still no result. No error, the log just say start mapping. Can any one with similar experience tell me how can I make it faster or is there anything wrong.
Below is my command:
/STAR-STAR_2.4.2a/bin/Linux_x86_64/STAR --outFilterIntronMotifs RemoveNoncanonicalUnannotated --runThreadN 2 --outTmpDir /pathdir/ --outSAMtype BAM SortedByCoordinate --genomeDir /pathfordatabaseformus/ --readFilesIn XXX.clean.fq.gz --readFilesCommand zcat
Thanks for all the guys who offer me help!
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