Fastq Groomer Processing Time

Question: Fastq Groomer Processing Time

6.8 years ago by

United States

I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from Illumina 1.3-1.7+ to Sanger and it is still processing after over 30 hrs. Is this a normal time frame for a FASTQ file this size ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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modified 6.8 years ago by Bossers, Alex • 240 • written 6.8 years ago by Matthew McCormack • 60

6.8 years ago by

Bossers, Alex • 240

Bossers, Alex • 240 wrote:

Matthew, yes we have seen such kind of long runs before (depending on server load). Happy most of our reads are now in 1.8+ format. You can parallelise the process by splitting the file in 4 or 6 and submit for grooming and afterwards merge them again... Alex ________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user- bounces@lists.bx.psu.edu] namens Matthew McCormack [mccormack@molbio.mgh.harvard.edu] Verzonden: maandag 27 februari 2012 21:13 To: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] FASTQ groomer processing time I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from Illumina 1.3-1.7+ to Sanger and it is still processing after over 30 hrs. Is this a normal time frame for a FASTQ file this size ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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