SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Running problem with cuffdiff john_nl Bioinformatics 2 02-16-2012 11:21 AM
The problem of running soapfusion louis7781x Bioinformatics 0 08-03-2011 02:44 AM
The problem of running soapfusion louis7781x Bioinformatics 0 08-03-2011 01:55 AM
problem running TopHat anecsulea RNA Sequencing 0 05-28-2010 12:44 AM
a tophat running problem clariet Bioinformatics 1 04-12-2010 05:05 AM

Reply
 
Thread Tools
Old 03-15-2012, 11:28 AM   #1
axiom7
Member
 
Location: Southwest

Join Date: Aug 2009
Posts: 14
Default Problem running cb_local; maybe manifest file?

Hi,
I am trying to run crossbow against a local fastq file that I have. I downloaded the hg18.jar file and I believe everything (or most everything) is configured correctly.

The command I execute is:

smwilson@axiom7:~/disk/crossbow-1.1.2$ ./cb_local --reference crossbow_refs/hg18 --input crossbow_refs/hg18/GTCA.manifest --output crossbow_refs/hg18/output --keep-all --cpus 4 --bowtie-args "-n2 -l28 -e 70 --trim5 4"

Contents of the manifest file is shown below, and the file exists:

smwilson@axiom7:~/disk/crossbow-1.1.2$ cat crossbow_refs/hg18/GTCA.manifest
/disk/smwilson/BerwickData_NCGR/input/GTCA.fastq
smwilson@axiom7:~/disk/crossbow-1.1.2$ ls -l /disk/smwilson/BerwickData_NCGR/input/GTCA.fastq

-rwxr-x--- 1 smwilson smwilson 2520434410 2012-03-08 14:22 /disk/smwilson/BerwickData_NCGR/input/GTCA.fastq

It seems as if Align.pl does not like my manifest file.

Thanks.
Susan

******
* Warning: No TOOLNAME file in tool directory: Bin
* Align.pl: s3cmd: found: , given:
* Align.pl: jar: found: /usr/bin/jar, given:
* Align.pl: hadoop: found: , given:
* Align.pl: wget: found: /usr/bin/wget, given:
* Align.pl: s3cfg:
* Align.pl: bowtie: found: /home/smwilson/disk/bowtie-0.12.7/bowtie, given: /home/smwilson/disk/bowtie-0.12.7/bowtie
* Align.pl: partition len: 1000000
* Align.pl: ref:
* Align.pl: quality: phred33
* Align.pl: truncate at: 0
* Align.pl: discard mate: 0
* Align.pl: discard reads < truncate len: 0
* Align.pl: SAM passthrough: 0
* Align.pl: Straight through: 0
* Align.pl: local index path: /disk/smwilson/crossbow-1.1.2/crossbow_refs/hg18/index/index
* Align.pl: counters: /home/smwilson/output_counters/counters.txt
* Align.pl: dest dir:
* Align.pl: bowtie args: --partition 1000000 --mm -t --hadoopout --startverbose -n2 -l28 -e 70 --trim5 4
* Align.pl: ls -al
* Align.pl: total 0
* drwxr-xr-x 2 smwilson smwilson 100 2012-03-15 13:16 .
* drwxr-xr-x 3 smwilson smwilson 60 2012-03-15 13:16 ..
* -rw-r--r-- 1 smwilson smwilson 0 2012-03-15 13:16 .tmp.29756
* -rw-r--r-- 1 smwilson smwilson 0 2012-03-15 13:16 .tmp.29780
* -rw-r--r-- 1 smwilson smwilson 0 2012-03-15 13:16 .tmp.29804
* Align.pl: Retrived 0 counters from previous stages
* Align.pl: Read first line of stdin:
* /disk/smwilson/BerwickData_NCGR/input/GTCA.fastq
* Bad number of read tokens ; expected 3 or 5:
* /disk/smwilson/BerwickData_NCGR/input/GTCA.fastq
******
axiom7 is offline   Reply With Quote
Old 03-15-2012, 11:47 AM   #2
axiom7
Member
 
Location: Southwest

Join Date: Aug 2009
Posts: 14
Default

I take it back. It seems as if Align.pl does not like the fastq file itself.
axiom7 is offline   Reply With Quote
Old 05-08-2013, 08:24 AM   #3
narain
Member
 
Location: Washington DC

Join Date: Aug 2011
Posts: 78
Default

Okay, so how do you run crossbow on a local file ? I tried it for .fastq.gz file too and it did not work. Any suggestions if you have sorted it out already ?
narain is offline   Reply With Quote
Reply

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 10:11 AM.


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