MapSplice error: open reads file

[thek71]

Hi all,
I am currently trying to use MapSplice and compare it with Tophat and SpliceMap. My reads are 60bp long single end in fasta format. When I try to run it I get the following:

bin directory: [/opt/MapSplice_1.15.1/bin/]
[Wed Mar 30 13:47:11 2011] Checking for chromosomes files or directory
[Wed Mar 30 13:47:11 2011] Checking for chromosomes files or directory passed
[Wed Mar 30 13:47:11 2011] Checking for Bowtie index files
[Wed Mar 30 13:47:11 2011] check reads format
[Wed Mar 30 13:47:11 2011] merge paired end reads remove short
[Wed Mar 30 13:47:12 2011] Mapping reads against P.patens_index with Bowtie
[Wed Mar 30 13:47:18 2011] Converting bowtie mapped to SAM format
[Wed Mar 30 13:47:18 2011] divide reads
[Wed Mar 30 13:47:19 2011] Mapping reads against P.patens_index with Bowtie
[Wed Mar 30 13:47:23 2011] reads all chromo sizes
[Wed Mar 30 13:47:24 2011] mapsplice_search
error: open reads file error
[FAILED]
Error: fmapsplice_search failed

Does anyone have any idea of what the problem might be???

Thank you very much

[greenshell]

can you check if the following files are empty or not exist

~/tmp/divided_reads.fa
~/tmp/unspliced_mapped_reads
~/tmp/unspliced_mapped_segments.sorted

seems the input reads file is small, can you also post the configuration you used to run MapSplice

[thek71]

The file unspliced_mapped_segments.sort does not exist, but the others are there and are not empty.
I have attached the configuration file.

[greenshell]

tested on similar data set, can't reproduce the same error

can you send first 10K lines of

~/tmp/unspliced_mapped_segments
~/tmp/divided_reads.fa
~/tmp/unspliced_mapped_reads
~/tmp/chrom_sizes

to [email protected]?

[valid1983]

Hi all!
I have a similar problem using just the example data from the website. Below the run command and the error message, run with Python 2.6.1 on Mac OSX 10.6.7.

$ python ./bin/mapsplice_segments.py -Q fq -o ./examples/1M_50bp_output_path/ -w 50 -c ./examples/chr20_sequence_index/ -u ./examples/1M_50bp_fastq.txt -B ./examples/chr20_sequence_index/index -L 25

[Wed May 25 15:33:52 2011] Preparing output location ./examples/1M_50bp_output_path//

[Wed May 25 15:33:52 2011] Beginning Mapsplice run (v1.15.2)
-----------------------------------------------
bin directory: [/Users/slunke/BioInf/Source/MapSplice_1.15.2/bin/]
[Wed May 25 15:33:52 2011] Checking for chromosomes files or directory
[Wed May 25 15:33:52 2011] Checking for chromosomes files or directory passed
[Wed May 25 15:33:52 2011] Checking for Bowtie index files
[Wed May 25 15:33:52 2011] check reads format
[Wed May 25 15:33:53 2011] merge paired end reads remove short
[Wed May 25 15:34:03 2011] Mapping reads against index with Bowtie
[Wed May 25 15:34:03 2011] Converting bowtie mapped to SAM format
[Wed May 25 15:34:03 2011] divide reads
error: open extended file error
[FAILED]
Error: divide reads failed

Any ideas anyone?? Can't figure out where I am going wrong...

Cheers
Seb

[greenshell]

Mac OSX version is at

http://www.netlab.uky.edu/p/bioinfo/MapSpliceDownload

Hi all!
I have a similar problem using just the example data from the website. Below the run command and the error message, run with Python 2.6.1 on Mac OSX 10.6.7.

$ python ./bin/mapsplice_segments.py -Q fq -o ./examples/1M_50bp_output_path/ -w 50 -c ./examples/chr20_sequence_index/ -u ./examples/1M_50bp_fastq.txt -B ./examples/chr20_sequence_index/index -L 25

[Wed May 25 15:33:52 2011] Preparing output location ./examples/1M_50bp_output_path//

[Wed May 25 15:33:52 2011] Beginning Mapsplice run (v1.15.2)
-----------------------------------------------
bin directory: [/Users/slunke/BioInf/Source/MapSplice_1.15.2/bin/]
[Wed May 25 15:33:52 2011] Checking for chromosomes files or directory
[Wed May 25 15:33:52 2011] Checking for chromosomes files or directory passed
[Wed May 25 15:33:52 2011] Checking for Bowtie index files
[Wed May 25 15:33:52 2011] check reads format
[Wed May 25 15:33:53 2011] merge paired end reads remove short
[Wed May 25 15:34:03 2011] Mapping reads against index with Bowtie
[Wed May 25 15:34:03 2011] Converting bowtie mapped to SAM format
[Wed May 25 15:34:03 2011] divide reads
error: open extended file error
[FAILED]
Error: divide reads failed

Any ideas anyone?? Can't figure out where I am going wrong...

Cheers
Seb