MapSplice V1.15.2 error

[paulorapazote]

Hi all

Im using Mapsplice with pair reads. I got the error message:


error: open entended file error

[FAILED]

Error: check reads format failed

Any idea to solve this error??

Regards

[Richard Finney]

It's probably "error: open extended file error", not "error: open entended file error"

Any previous output? , there's usually a complete narrative which looks like this example ...

[Thu Jun 21 11:17:06 2012] Checking for chromosomes files or directory
[Thu Jun 21 11:17:07 2012] Checking for chromosomes files or directory passed
[Thu Jun 21 11:17:07 2012] Checking for Bowtie index files
[Thu Jun 21 11:17:07 2012] check reads format
[Thu Jun 21 11:19:23 2012] merge paired end reads remove short
[Thu Jun 21 11:27:15 2012] Mapping reads against bowtie_index_basename with Bowtie

What is the name of the last output in the logs directory ???

The program bin/mapsplice_segments.py contains the "check reads format failed" strings at line 4946 of 7830 ...

    if DEBUG == 1:
        print >> sys.stderr, "[%s] check reads format" % dividereads_cmd
    #print >> sys.stderr, "[%s] divide reads" % dividereads_cmd
    try:
        retcode = subprocess.call(dividereads_cmd, stdout=mapsplice_log)

        if retcode > 0:
            print >> sys.stderr, fail_str, "Error: check reads format failed"
            exit(1)

So it's dividereads_cmd is failing.

It looks like there's a nice debug command in the "if DEBUG == 1" clause on line 4939.

Try turning on DEBUG = 1 on line 120 of the python source file "bin/mapsplice_segments.py", then re-run it. That should give you a better hint.

Remember to set the path to point to the mapsplice "bin" directory in addition to your regular path.

[paulorapazote]

Hi

Problem solved. I forgot to put the path of the read_end2:

I put "path/read_end1, read_end2" but the correct is "path/read_end1, path/read_end2".

Many thanks,

P