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Old 07-07-2011, 11:22 AM   #1
swbiggs4
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Default cuffmerge crashes when converting gtf files to sam files

Hello,

I am fairly new to cufflinks and I am trying to use cuffmerge to merge assemblies made with cufflinks. I am running the command:

cuffmerge -s /data/sequence/mm9/mm9.fa -g /data/annotation/mm9_ucsc_known.gtf -p 4 assemblies.txt

and I get the following output:


[Thu Jul 7 15:19:22 2011] Preparing output location ./merged_asm/
[Thu Jul 7 15:19:36 2011] Converting GTF files to SAM
[15:19:37] Loading reference annotation.
[FAILED]
Error: could not execute gtf_to_sam

When trying to use the gtf_to_sam binary to convert cufflinks gtf files to sam files, I just get a cryptic "Bus Error" message. It doesn't seem to matter whether I try to convert cufflinks gtf files or an annotation GTF file of UCSC known gene ids downloaded from the UCSC browser. Has anyone encountered a similar problem before? I have cufflinks version 1.0.3 installed on Mac OS X. I have tried both compiling from source and downloading the precompiled binaries from the cufflinks site.
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Old 07-13-2011, 06:13 AM   #2
ngomez
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*Bump - I'm having the same error. Any help would be appreciated.
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Old 07-13-2011, 04:26 PM   #3
joseph
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I sent numerous e-mails to the authors, but still no response.
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Old 09-29-2011, 08:50 AM   #4
ef10k
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Has anyone figured out how to solve this problem? I am getting the same error (with cufflinks v1.1.0, attempting to merge transcripts.gtfs generated by cufflinks).
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Old 09-29-2011, 09:39 AM   #5
damiankao
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Try the solution I posted at:
http://seqanswers.com/forums/showthread.php?t=11694
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Old 09-29-2011, 10:34 AM   #6
ef10k
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Thanks for the reply, damiankao. However, the fix that you described didn't work for me (by editing the cuffmerge script from v1.0.2 - as far as I can tell, the header sorting issue that your fix addresses has been resolved in v1.1.0).

Specifically, the output that I get is:

[Thu Sep 29 14:14:05 2011] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Sep 29 14:14:05 2011] Preparing output location transcripts_merge/
[Thu Sep 29 14:14:19 2011] Converting GTF files to SAM
[14:14:19] Loading reference annotation.
[FAILED]
Error: could not execute gtf_to_sam


Poking around in the cuffmerge script, one can see that the error is generated by this function:

Code:
def gtf_to_sam(gtf_filename):

    sam_out = tmp_name("gtf2sam_")

    cmd = ["gtf_to_sam"]
    cmd.append("-F")
    cmd.append(gtf_filename)
    cmd.append(sam_out)
    try:
        print >> run_log, " ".join(cmd)
        ret = subprocess.call(cmd)
        if ret != 0:
            print >> sys.stderr, fail_str, "Error: could not execute gtf_to_sam"
            exit(1)
However, I really don't know much about python and don't have a good idea of what this is doing. Does anyone have any ideas about what's going wrong here?
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Old 10-03-2011, 02:32 AM   #7
damiankao
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It looks like the gtf_to_sam script is not working. Do you have it in your path? Have you tried merging only the cufflinks gtf outputs together? Maybe the USCS gtf is not formatted in a way that cuffmerge can read? You can try running gtf_to_sam on a gtf file without cuffmerge and see if that works.
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Old 10-03-2011, 08:32 AM   #8
ZhengXia
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As damiankao said, maybe you can try the gtf provided in the Cufflinks website.
Quote:
Originally Posted by damiankao View Post
It looks like the gtf_to_sam script is not working. Do you have it in your path? Have you tried merging only the cufflinks gtf outputs together? Maybe the USCS gtf is not formatted in a way that cuffmerge can read? You can try running gtf_to_sam on a gtf file without cuffmerge and see if that works.
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Old 10-18-2011, 08:27 AM   #9
SEQond
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did the Cufflinks website GTF solve the problem?
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Old 10-24-2011, 12:23 PM   #10
dweebis
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Hi Guys -

I'm having essentially the same problem. I'm trying to merger together just two transcript.gtf files usig the following command:

Quote:
>cuffmerge -s ~/Work/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa assemblies.txt
And I get the following output:
Quote:
[Mon Oct 24 15:18:45 2011] Beginning transcriptome assembly merge
-------------------------------------------

[Mon Oct 24 15:18:45 2011] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Mon Oct 24 15:18:49 2011] Converting GTF files to SAM
[15:18:49] Loading reference annotation.
*** buffer overflow detected ***: gtf_to_sam terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7f52eb7e8217]
/lib/libc.so.6(+0xfe0d0)[0x7f52eb7e70d0]
/lib/libc.so.6(+0xfcf87)[0x7f52eb7e5f87]
gtf_to_sam[0x406fb0]
gtf_to_sam[0x408c84]
gtf_to_sam[0x409226]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f52eb707c4d]
gtf_to_sam[0x406ab9]
======= Memory map: ========
00400000-004f3000 r-xp 00000000 08:01 8260509 /usr/local/cufflinks-1.1.0/bin/gtf_to_sam
006f2000-006f3000 r--p 000f2000 08:01 8260509 /usr/local/cufflinks-1.1.0/bin/gtf_to_sam
006f3000-006f5000 rw-p 000f3000 08:01 8260509 /usr/local/cufflinks-1.1.0/bin/gtf_to_sam
006f5000-00700000 rw-p 00000000 00:00 0
00e06000-096ea000 rw-p 00000000 00:00 0 [heap]
7f52eb4e1000-7f52eb4e8000 r-xp 00000000 08:01 9178866 /lib/librt-2.11.1.so
7f52eb4e8000-7f52eb6e7000 ---p 00007000 08:01 9178866 /lib/librt-2.11.1.so
7f52eb6e7000-7f52eb6e8000 r--p 00006000 08:01 9178866 /lib/librt-2.11.1.so
7f52eb6e8000-7f52eb6e9000 rw-p 00007000 08:01 9178866 /lib/librt-2.11.1.so
7f52eb6e9000-7f52eb863000 r-xp 00000000 08:01 9178850 /lib/libc-2.11.1.so
7f52eb863000-7f52eba62000 ---p 0017a000 08:01 9178850 /lib/libc-2.11.1.so
7f52eba62000-7f52eba66000 r--p 00179000 08:01 9178850 /lib/libc-2.11.1.so
7f52eba66000-7f52eba67000 rw-p 0017d000 08:01 9178850 /lib/libc-2.11.1.so
7f52eba67000-7f52eba6c000 rw-p 00000000 00:00 0
7f52eba6c000-7f52eba84000 r-xp 00000000 08:01 9178864 /lib/libpthread-2.11.1.so
7f52eba84000-7f52ebc83000 ---p 00018000 08:01 9178864 /lib/libpthread-2.11.1.so
7f52ebc83000-7f52ebc84000 r--p 00017000 08:01 9178864 /lib/libpthread-2.11.1.so
7f52ebc84000-7f52ebc85000 rw-p 00018000 08:01 9178864 /lib/libpthread-2.11.1.so
7f52ebc85000-7f52ebc89000 rw-p 00000000 00:00 0
7f52ebc89000-7f52ebc9f000 r-xp 00000000 08:01 9175119 /lib/libgcc_s.so.1
7f52ebc9f000-7f52ebe9e000 ---p 00016000 08:01 9175119 /lib/libgcc_s.so.1
7f52ebe9e000-7f52ebe9f000 r--p 00015000 08:01 9175119 /lib/libgcc_s.so.1
7f52ebe9f000-7f52ebea0000 rw-p 00016000 08:01 9175119 /lib/libgcc_s.so.1
7f52ebea0000-7f52ebf22000 r-xp 00000000 08:01 9178854 /lib/libm-2.11.1.so
7f52ebf22000-7f52ec121000 ---p 00082000 08:01 9178854 /lib/libm-2.11.1.so
7f52ec121000-7f52ec122000 r--p 00081000 08:01 9178854 /lib/libm-2.11.1.so
7f52ec122000-7f52ec123000 rw-p 00082000 08:01 9178854 /lib/libm-2.11.1.so
7f52ec123000-7f52ec219000 r-xp 00000000 08:01 5901999 /usr/lib/libstdc++.so.6.0.13
7f52ec219000-7f52ec419000 ---p 000f6000 08:01 5901999 /usr/lib/libstdc++.so.6.0.13
7f52ec419000-7f52ec420000 r--p 000f6000 08:01 5901999 /usr/lib/libstdc++.so.6.0.13
7f52ec420000-7f52ec422000 rw-p 000fd000 08:01 5901999 /usr/lib/libstdc++.so.6.0.13
7f52ec422000-7f52ec437000 rw-p 00000000 00:00 0
7f52ec437000-7f52ec44d000 r-xp 00000000 08:01 9175234 /lib/libz.so.1.2.3.3
7f52ec44d000-7f52ec64c000 ---p 00016000 08:01 9175234 /lib/libz.so.1.2.3.3
7f52ec64c000-7f52ec64d000 r--p 00015000 08:01 9175234 /lib/libz.so.1.2.3.3
7f52ec64d000-7f52ec64e000 rw-p 00016000 08:01 9175234 /lib/libz.so.1.2.3.3
7f52ec64e000-7f52ec662000 r-xp 00000000 08:01 5937267 /usr/lib/libboost_thread.so.1.40.0
7f52ec662000-7f52ec861000 ---p 00014000 08:01 5937267 /usr/lib/libboost_thread.so.1.40.0
7f52ec861000-7f52ec863000 r--p 00013000 08:01 5937267 /usr/lib/libboost_thread.so.1.40.0
7f52ec863000-7f52ec864000 rw-p 00015000 08:01 5937267 /usr/lib/libboost_thread.so.1.40.0
7f52ec864000-7f52ec884000 r-xp 00000000 08:01 9178847 /lib/ld-2.11.1.so
7f52eca5d000-7f52eca63000 rw-p 00000000 00:00 0
7f52eca7f000-7f52eca83000 rw-p 00000000 00:00 0
7f52eca83000-7f52eca84000 r--p 0001f000 08:01 9178847 /lib/ld-2.11.1.so
7f52eca84000-7f52eca85000 rw-p 00020000 08:01 9178847 /lib/ld-2.11.1.so
7f52eca85000-7f52eca86000 rw-p 00000000 00:00 0
7fff7d7fe000-7fff7d81f000 rw-p 00000000 00:00 0 [stack]
7fff7d9ff000-7fff7da00000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
[FAILED]
Error: could not execute gtf_to_sam
I get essentially the same error running gtf_to_sam directly. System call failures are out of my depth, has there been any more progress on this problem?
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Old 10-30-2011, 05:25 AM   #11
gpertea
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It turns out there is a trivial fix for at least some of the crashes reported here (just increasing the cigar[] buffer size in gtf_to_sam.cpp and recompile). Until the next official Cufflinks package release, those affected by this problem can use these patched binaries to replace the gtf_to_sam program that came with the 1.1.0 distribution:

For Mac OSX:
ftp://ftp.cbcb.umd.edu/pub/software/..._to_sam.OSX.gz

For Linux x86_64:
ftp://ftp.cbcb.umd.edu/pub/software/...o_sam.Linux.gz

(please remember to rename the file to gtf_to_sam after decompressing it)

The patched source code is here:
ftp://ftp.cbcb.umd.edu/pub/software/misc/gtf_to_sam.cpp
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Old 05-30-2012, 08:20 AM   #12
gokhulkrishnakilaru
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Quote:
Originally Posted by ef10k View Post
Thanks for the reply, damiankao. However, the fix that you described didn't work for me (by editing the cuffmerge script from v1.0.2 - as far as I can tell, the header sorting issue that your fix addresses has been resolved in v1.1.0).

Specifically, the output that I get is:

[Thu Sep 29 14:14:05 2011] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Sep 29 14:14:05 2011] Preparing output location transcripts_merge/
[Thu Sep 29 14:14:19 2011] Converting GTF files to SAM
[14:14:19] Loading reference annotation.
[FAILED]
Error: could not execute gtf_to_sam


Poking around in the cuffmerge script, one can see that the error is generated by this function:

Code:
def gtf_to_sam(gtf_filename):

    sam_out = tmp_name("gtf2sam_")

    cmd = ["gtf_to_sam"]
    cmd.append("-F")
    cmd.append(gtf_filename)
    cmd.append(sam_out)
    try:
        print >> run_log, " ".join(cmd)
        ret = subprocess.call(cmd)
        if ret != 0:
            print >> sys.stderr, fail_str, "Error: could not execute gtf_to_sam"
            exit(1)
However, I really don't know much about python and don't have a good idea of what this is doing. Does anyone have any ideas about what's going wrong here?
Change your
Quote:
cmd = ["gtf_to_sam"]
to
Quote:
cmd = ["/path_of the_program/gtf_to_sam"]
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Old 08-19-2014, 01:18 PM   #13
thickrick99
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Sorry to bring back an old thread but has anyone found a solution for this yet?? I posted in the RNA-seq forum and still have no replies but I am facing the same issue and can't seem to find a solution on the internet. Any ideas??
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Old 08-21-2015, 02:17 PM   #14
Gonza
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Hello All,

I am having the same problem. Thanks for the help



[Fri Aug 21 18:11:42 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Aug 21 18:11:42 2015] Preparing output location /home3/gonzalo/Petunia/03_cuffmerge/
[Fri Aug 21 18:12:44 2015] Converting GTF files to SAM
[18:12:44] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=Peaxi162Scf00001g00028.1
[FAILED]
Error: could not execute gtf_to_sam
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Old 11-04-2015, 09:54 AM   #15
bbm
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Anybody knows how to fix this?
I ran into the same problem. I'm using cufflinks 2.2.1
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Old 02-07-2017, 02:57 PM   #16
leejimmy93
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Did anyone fixed the problem? same problem happened here.
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Old 02-08-2017, 11:41 AM   #17
Gonza
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Default Cufflinks duplicated genes error

Hi all,

I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

G
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Old 02-09-2017, 03:37 PM   #18
leejimmy93
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Quote:
Originally Posted by Gonza View Post
Hi all,

I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

G
Hi, do you mean the duplicated gene ID in the reference gtf file or the gtf file generated by cufflinks? Also was your reference gtf file sorted? Can you please send me a screenshot of the gtf file that works and that doesn't work?

Thank you very much!
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Old 02-15-2017, 05:24 AM   #19
Gonza
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Hi,

This is what i was getting.



[Fri Jan 6 12:35:41 2017] Beginning transcriptome assembly merge

-------------------------------------------

[Fri Jan 6 12:35:41 2017] Preparing output location ./merged_asm/

[Fri Jan 6 12:36:23 2017] Converting GTF files to SAM

[12:36:23] Loading reference annotation.

GFF Error: duplicate/invalid 'transcript' feature ID=Peaxi162Scf00002g00014.1

[FAILED]

Error: could not execute gtf_to_sam




Once i started to used an updated GTF/GFF file i had no problem. Not sure what species you're working with, but this problem will not occur if you are using one with well annotated features.

Good luck
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Old 02-15-2017, 03:47 PM   #20
leejimmy93
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It turned out my problem was caused by the reference gtf/gff file too. Thank you very much!
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