MapSplice error

[sean760305]

hello,
I am running MapSplice and I am able to get the output files, but there is empty in my best_junction.bed file.

Furthermore, I got some error messenger form MapSplice:

[Thu Jun 28 04:07:56 2012] Beginning Mapsplice run (v1.15.2)
-----------------------------------------------
bin directory: [/home/biongs158/Mapsplice_1.15.2/bin/]
[Thu Jun 28 04:07:56 2012] Checking for chromosomes files or directory
[Thu Jun 28 04:07:56 2012] Checking for chromosomes files or directory passed
[Thu Jun 28 04:07:56 2012] Checking for Bowtie index files
[Thu Jun 28 04:07:56 2012] check reads format
[Thu Jun 28 04:08:43 2012] merge paired end reads remove short
[Thu Jun 28 04:15:14 2012] Mapping reads against SRS000047_chr11_no_n with Bowtie
[Thu Jun 28 04:20:06 2012] Converting bowtie mapped to SAM format
[Thu Jun 28 04:20:52 2012] divide reads
[Thu Jun 28 04:36:48 2012] Mapping reads against SRS000047_chr11_no_n with Bowtie
[Thu Jun 28 04:50:55 2012] sort segmentbwt
[Thu Jun 28 05:00:54 2012] reads all chromo sizes
[Thu Jun 28 05:00:56 2012] mapsplice_search
[Thu Jun 28 05:14:51 2012] Aligning spliced reads
[Thu Jun 28 05:28:32 2012] mapsplice_report
[Thu Jun 28 05:35:56 2012] remove index of sam
[Thu Jun 28 05:35:59 2012] sort segmentbwt
[Thu Jun 28 05:36:01 2012] convert sam files to junctions
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create
[Thu Jun 28 05:36:03 2012] sort by name
[Thu Jun 28 05:36:33 2012] Remove duplication of sam
[Thu Jun 28 05:37:09 2012] Filtering junctions
[Thu Jun 28 05:37:09 2012] Remove duplication of sam
[Thu Jun 28 05:37:12 2012] Filter Reads By Canon Noncanon
[Thu Jun 28 05:37:12 2012] convert sam files to junctions
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create
[Thu Jun 28 05:37:13 2012] convert sam files to junctions
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create
[Thu Jun 28 05:37:14 2012] filter junction by min mis and min lpq
[Thu Jun 28 05:37:14 2012] filter junc by ROC argu noncanonical
[Thu Jun 28 05:37:14 2012] filter junction by min mis and min lpq
[Thu Jun 28 05:37:14 2012] convert junction file to bed format
[Thu Jun 28 05:37:15 2012] Filter Sam By junction
[Thu Jun 28 05:37:16 2012] Merging all sam files
[Thu Jun 28 05:37:20 2012] convert sam files to junctions
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_S_create
[Thu Jun 28 05:37:26 2012] convert junction file to bed format
[Thu Jun 28 05:37:26 2012] sort segmentbwt
[Thu Jun 28 05:37:34 2012] Add tags to sam file
[Thu Jun 28 05:47:31 2012] combine to final sam

[Thu Jun 28 05:49:16 2012] Finishing Mapsplice run (time used: 1:41:20.265268)

Does anyone have these error?
Hope you can help me，thanks a lot!

[wuj]

Please email the author, I think he will be glad to help you.