SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to evaluate MIRA assembly kp5091 Bioinformatics 30 11-19-2013 07:19 PM
how to evaluate if the replicates are good capricy Bioinformatics 4 11-05-2013 03:01 PM
RNAseq time series data w/ controls for each time point Mocca RNA Sequencing 2 08-07-2013 11:12 PM
how to evaluate raw data oceanxie Bioinformatics 1 04-15-2011 01:52 AM
How to evaluate assembly quality? sunyu1357 Bioinformatics 2 02-15-2010 05:49 AM

Reply
 
Thread Tools
Old 09-16-2015, 07:32 PM   #1
cindylanzao
Member
 
Location: chicago

Join Date: Nov 2012
Posts: 19
Smile 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!
cindylanzao is offline   Reply With Quote
Old 09-18-2015, 07:25 AM   #2
alexdobin
Senior Member
 
Location: NY

Join Date: Feb 2009
Posts: 161
Default

Quote:
Originally Posted by cindylanzao View Post
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!
Hi @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
alexdobin is offline   Reply With Quote
Old 09-20-2015, 05:56 PM   #3
cindylanzao
Member
 
Location: chicago

Join Date: Nov 2012
Posts: 19
Question Thanks for your reply

Quote:
Originally Posted by alexdobin View Post
Hi @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
Thanks 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!
cindylanzao is offline   Reply With Quote
Old 09-22-2015, 08:17 AM   #4
alexdobin
Senior Member
 
Location: NY

Join Date: Feb 2009
Posts: 161
Default

Quote:
Originally Posted by cindylanzao View Post
Thanks 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!
Hi @cindylanzao,

please post or email me the Log.out file from the failed single sample 12-thread run.

Cheers
Alex
alexdobin is offline   Reply With Quote
Old 09-22-2015, 06:15 PM   #5
cindylanzao
Member
 
Location: chicago

Join Date: Nov 2012
Posts: 19
Unhappy

Quote:
Originally Posted by alexdobin View Post
Hi @cindylanzao,

please post or email me the Log.out file from the failed single sample 12-thread run.

Cheers
Alex
Thanks for your help, but the project is in a hurry, so I have decided to change to tophat as the aligner, and have deleted all the related output file from STAR.
cindylanzao is offline   Reply With Quote
Reply

Tags
mouse, rna-seq, star aligner

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:30 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO