MapSplice 1.15.1 error

[Irina Pulyakhina]

Hi everyone,

I'm running MapSplice 1.15.1 and get an error:

[Thu Sep 15 11:19:36 2011] Preparing output location /home/ipulyakhina/Programs/MapSplice_1.15.2/RESULTS//

[Thu Sep 15 11:19:36 2011] Beginning Mapsplice run (v1.15.2)
-----------------------------------------------
bin directory: [/home/ipulyakhina/Programs/MapSplice_1.15.2/bin/]
[Thu Sep 15 11:19:36 2011] Checking for chromosomes files or directory
[Thu Sep 15 11:19:36 2011] Checking for chromosomes files or directory passed
[Thu Sep 15 11:19:36 2011] Checking for Bowtie index files
[Thu Sep 15 11:19:36 2011] Indexing chromosome sequences
[Thu Sep 15 11:23:46 2011] check reads format
[Thu Sep 15 11:23:46 2011] merge paired end reads remove short
[Thu Sep 15 11:23:46 2011] Converting bowtie mapped to SAM format
[Thu Sep 15 11:23:46 2011] divide reads
[Thu Sep 15 11:23:46 2011] Mapping reads against with Bowtie
[FAILED]
Error: could not execute Bowtie

Of course I have the latest version of bowtie, I've written the path to bowtie in the .bashrc and I can execute it from the command line.

Does anyone know what is the problem?

Thanks in advance,
Irina

[greenshell]

Can you check error message

in
~/logs/unspliced_segments.log
or
~/logs/unspliced_reads.log
?

[Irina Pulyakhina]

Thank you for your reply! I found out the problem and MapSplice is passing through this point no, but I do get the other error:

=======================
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
=======================

It's being thrown at the step of "Indexing chromosome sequences". Maybe you know what the problem is?

I don't have any ~/logs/unspliced_reads.log file; the ~/logs/unspliced_segments.log is:
=======================
# reads processed: 807695920
# reads with at least one reported alignment: 184993777 (22.90%)
# reads that failed to align: 622702143 (77.10%)
Reported 1875904633 alignments to 1 output stream(s)
=======================

Thanks in advance!

[greenshell]

Thank you for your reply! I found out the problem and MapSplice is passing through this point no, but I do get the other error:

=======================
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
=======================

It's being thrown at the step of "Indexing chromosome sequences". Maybe you know what the problem is?

I don't have any ~/logs/unspliced_reads.log file; the ~/logs/unspliced_segments.log is:
=======================
# reads processed: 807695920
# reads with at least one reported alignment: 184993777 (22.90%)
# reads that failed to align: 622702143 (77.10%)
Reported 1875904633 alignments to 1 output stream(s)
=======================

Thanks in advance!

This means no original junctions generated, can you send ~/logs/ directory to mapsplice (at) netlab.uky.edu?

[Irina Pulyakhina]

Yes, I've just sent it, the email "MapSplice logs directory" to [email protected] (just netlab.uky.edu didn't work). Thank again!