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Old 03-30-2011, 04:06 AM   #1
thek71
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Location: Freiburg

Join Date: Mar 2011
Posts: 4
Default MapSplice error: open reads file

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
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Old 03-30-2011, 05:58 AM   #2
greenshell
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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
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Old 03-30-2011, 06:20 AM   #3
thek71
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The file unspliced_mapped_segments.sort does not exist, but the others are there and are not empty.
I have attached the configuration file.
Attached Files
File Type: txt single_tmp.txt (7.4 KB, 24 views)

Last edited by thek71; 03-30-2011 at 06:24 AM.
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Old 03-30-2011, 06:46 AM   #4
greenshell
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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 mapsplice@netlab.uky.edu?
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Old 05-24-2011, 09:51 PM   #5
valid1983
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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
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Old 05-25-2011, 05:51 AM   #6
greenshell
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Mac OSX version is at

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


Quote:
Originally Posted by valid1983 View Post
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

Last edited by greenshell; 05-25-2011 at 07:14 AM.
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