cuffmerge crashes when converting gtf files to sam files

[swbiggs4]

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.

[ngomez]

*Bump - I'm having the same error. Any help would be appreciated.

[joseph]

I sent numerous e-mails to the authors, but still no response.

[ef10k]

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).

[damiankao]

Try the solution I posted at:

http://seqanswers.com/forums/showthread.php?t=11694

[ef10k]

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:

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?

[damiankao]

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.

[ZhengXia]

As damiankao said, maybe you can try the gtf provided in the Cufflinks website.

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.

[SEQond]

did the Cufflinks website GTF solve the problem?

[dweebis]

Hi Guys -

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

>cuffmerge -s ~/Work/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa assemblies.txt

And I get the following output:

[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?

[gpertea]

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

[gokhulkrishnakilaru]

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:

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

cmd = ["gtf_to_sam"]

to

cmd = ["/path_of the_program/gtf_to_sam"]

[thickrick99]

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??

[Gonza]

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

[bbm]

Anybody knows how to fix this?
I ran into the same problem. I'm using cufflinks 2.2.1