Mapsplice Error

Question

[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 SRS000047chr11no_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 SRS000047chr11no_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::lengtherror' what(): basicstring::Screate

[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::lengtherror' what(): basicstring::Screate

[Thu Jun 28 05:37:13 2012] convert sam files to junctions

terminate called after throwing an instance of 'std::lengtherror' what(): basicstring::Screate

[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::lengtherror' what(): basicstring::Screate

[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!

Answer 1

[Vikas Bansal]

Here is something I found with similar error. Have a look at the answer and comments. -

It means you tried to create a string bigger than std::string::max_size().

http://msdn.microsoft.com/en-us/library/as4axahk(VS.80).aspx

A exception of type length_error Class is thrown when an operation produces a string with a length greater than the maximum size.

Could you paste the exact command you used to run MapSplice?

Answer 2

[sean760305]

My command is: python bin/mapsplicesegments.py config/SRS000047chr11.cfg

and my command is all in a config(cfg) file.

reads_file = hs_reads/ERS008775/ERR011384_1.fastq,hs_reads/ERS008775/ERR011384_2.fastq

chromosome_files_dir = bowtie-0.12.7/SRS000047/genomes/SRS000047_chr11_no_n.fa

Bowtieidx = bowtie-0.12.7/SRS000047/indexes/SRS000047_chr11_no_n

output_dir = out/SRS000047/chr11

reads_format = FASTQ

paired_end = YES

segment_length = 25

junction_type = non-canonical

fusion_junction_type = non-canonical

anchor_length = 8

remove_temp_files = no

segment_mismatches = 1

splice_mismatches = 1

remap_mismatches = 2

min_intron_length = 1

max_intron_length = 200000

threads = 4

max_hits = 4

max_insert = 3

search_whole_chromosome = no