SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
New version of MapSplice error repinementer Bioinformatics 16 04-08-2016 12:21 AM
MapSplice 1.15.2 error hardi RNA Sequencing 0 11-16-2011 10:25 PM
MapSplice 1.15.1 error Irina Pulyakhina RNA Sequencing 4 09-27-2011 02:09 AM
MapSplice error: open reads file thek71 RNA Sequencing 5 05-25-2011 05:51 AM
MapSplice error hdinhdp RNA Sequencing 2 03-07-2011 08:49 AM

Reply
 
Thread Tools
Old 06-21-2012, 07:29 AM   #1
paulorapazote
Member
 
Location: Scotland - TJHI

Join Date: May 2012
Posts: 19
Default MapSplice V1.15.2 error

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
paulorapazote is offline   Reply With Quote
Old 06-21-2012, 08:25 AM   #2
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 699
Default

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 ...
Code:
    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.
Richard Finney is offline   Reply With Quote
Old 07-06-2012, 01:18 AM   #3
paulorapazote
Member
 
Location: Scotland - TJHI

Join Date: May 2012
Posts: 19
Default

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
paulorapazote is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:59 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO