Problem running cb_local; maybe manifest file?

[axiom7]

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]

I take it back. It seems as if Align.pl does not like the fastq file itself.

[narain]

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 ?