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>
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>
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