MapSplice error

[hdinhdp]

Hello,

I am currently trying to run MapSplice. I was able to get the output files, but fear that there might be something wrong since I have been seeing the following error msg every time I run the software. Have anyone also experience this as well?

<code>

[Fri Feb 4 13:32:57 2011] Beginning Mapsplice run (v1.14.1)
-----------------------------------------------
bin directory: [/home/dinh/tools/MapSplice_1.14.1/bin/]
[Fri Feb 4 13:32:57 2011] Preparing output location /home/dinh/MapSplice_Out/
[Fri Feb 4 13:32:58 2011] Checking for chromosomes files or directory
base name of chromosome file not consistent with chromosome name
base chromosoem file name:mm9
chromosome name:chr10
[Fri Feb 4 13:32:58 2011] format chromosome files
[Fri Feb 4 13:38:02 2011] Checking for Bowtie index files
[Fri Feb 4 13:38:02 2011] merge paired end reads
[Fri Feb 4 13:39:52 2011] Mapping reads against mm9 with Bowtie
[Fri Feb 4 14:05:58 2011] Converting bowtie mapped to SAM format
[Fri Feb 4 14:08:08 2011] divide reads
[Fri Feb 4 14:12:43 2011] Mapping reads against mm9 with Bowtie
[Fri Feb 4 17:26:39 2011] sort segmentbwt
[Fri Feb 4 17:44:28 2011] reads all chromo sizes
[Fri Feb 4 17:45:02 2011] mapsplice_search
[Fri Feb 4 18:03:10 2011] Aligning spliced reads
sort: read failed: -: Bad file descriptor
sh: .txt: command not found
sh: .txt: command not found
sort: read failed: -: Bad file descriptor
sh: .txt.fixed: command not found
sh: .txt.fixed: command not found
sort: read failed: -: Bad file descriptor
sh: .txt: command not found
sh: .txt: command not found
sort: read failed: -: Bad file descriptor
sh: .txt.fixed: command not found
sh: .txt.fixed: command not found
sort: read failed: -: Bad file descriptor
sh: .txt: command not found
sh: .txt: command not found
tac: cannot open `home/dinh/MapSplice_Out/tmp/single_anchored_head//y_%coordList' for reading: No such file or directory
sh: .txt: command not found
sh: .txt.rev: command not found
mv: missing destination file operand after `home/dinh/MapSplice_Out/tmp/single_anchored_head//y_%coordList'
Try `mv --help' for more information.
sh: .txt.rev: command not found
sh: .txt: command not found
sort: read failed: -: Bad file descriptor
sh: .txt.fixed: command not found
sh: .txt.fixed: command not found
[Fri Feb 4 18:50:28 2011] mapsplice_report
[Fri Feb 4 19:04:44 2011] remove index of sam
[Fri Feb 4 19:04:48 2011] sort segmentbwt
[Fri Feb 4 19:04:53 2011] Aligning fusion spliced reads
[Fri Feb 4 19:13:33 2011] Merging all sam files
[Fri Feb 4 19:13:33 2011] sort segmentbwt
[Fri Feb 4 19:13:33 2011] separate combined fusion to unique and multiple mapped reads
[Fri Feb 4 19:13:34 2011] convert fusion sam file to junctions
[Fri Feb 4 19:13:34 2011] filter fusion junction by min mismatch
[Fri Feb 4 19:13:34 2011] convert sam files to junctions
[Fri Feb 4 19:13:59 2011] sort by name
[Fri Feb 4 19:15:15 2011] Remove duplication of sam
[Fri Feb 4 19:16:44 2011] Filtering junctions
[Fri Feb 4 19:16:45 2011] Remove duplication of sam
[Fri Feb 4 19:16:50 2011] Filter Reads By Canon Noncanon
[Fri Feb 4 19:16:57 2011] convert sam files to junctions
[Fri Feb 4 19:17:26 2011] convert sam files to junctions
[Fri Feb 4 19:17:49 2011] filter junction by min mis and min lpq
[Fri Feb 4 19:17:49 2011] filter junc by ROC argu noncanonical
[Fri Feb 4 19:17:49 2011] Merging all sam files
[Fri Feb 4 19:18:05 2011] Separate Spliced UnSpliced sam
[Fri Feb 4 19:18:33 2011] Synthetic junctions sequence
[Fri Feb 4 19:18:43 2011] Checking for Bowtie index files
[Fri Feb 4 19:18:43 2011] Indexing chromosome sequences
[Fri Feb 4 19:19:01 2011] Mapping reads against syn_idx_prefix with Bowtie
[Fri Feb 4 19:24:29 2011] Converting juncdb bowtie mapped to SAM format
[Fri Feb 4 19:24:34 2011] sort segmentbwt
[Fri Feb 4 19:24:36 2011] Remove duplication of sam
[Fri Feb 4 19:24:37 2011] Filter Reads By Canon Noncanon
[Fri Feb 4 19:24:38 2011] Merging all sam files
[Fri Feb 4 19:24:53 2011] sort segmentbwt
[Fri Feb 4 19:25:18 2011] Remove duplication of sam
[Fri Feb 4 19:25:48 2011] Filter Reads By Canon Noncanon
[Fri Feb 4 19:26:10 2011] convert sam files to junctions
[Fri Feb 4 19:27:07 2011] Merging all sam files
[Fri Feb 4 19:27:23 2011] convert sam files to junctions
[Fri Feb 4 19:27:55 2011] filter junction by min mis and min lpq
[Fri Feb 4 19:27:55 2011] filter junction by min mis and min lpq
[Fri Feb 4 19:27:55 2011] convert junction file to bed format
[Fri Feb 4 19:27:57 2011] Filter Sam By junction
[Fri Feb 4 19:28:27 2011] convert sam files to junctions
[Fri Feb 4 19:28:58 2011] convert junction file to bed format
[Fri Feb 4 19:29:00 2011] sort segmentbwt
[Fri Feb 4 19:29:24 2011] Add tags to sam file
[Fri Feb 4 19:30:59 2011] combine to final sam

[Fri Feb 4 19:31:58 2011] Finishing Mapsplice run (time used: 5:59:01.072387)
-----------------------------------------------
</code>

[greenshell]

The chromosome file name and first line in chromosome file seems not consistent by the log

Can you show the first line of the chromosome file chr10 and the file name?

[hdinhdp]

you're right! There were some .fa files in the same folder who's chromosome name and filename don't match.

Thanks!