can't run cuffmerge

[moriah]

Hi All,

I am trying to run cuffmege and keep getting this error

cuffmerge -g hg19_refseq.gtf -s hg19_new.fa -p 8 assemblies.txt


[Sun Mar 11 16:26:35 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Sun Mar 11 16:26:35 2012] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/private/apps/bin/cuffmerge", line 573, in ?
sys.exit(main())
File "/private/apps/bin/cuffmerge", line 543, in main
chrom_info = get_gtf_chrom_info(gtf, chrom_info)
File "/private/apps/bin/cuffmerge", line 476, in get_gtf_chrom_info
left = int(cols[3])
ValueError: invalid literal for int(): 5chr1


Does somebody know why?

Thanks,
Moriah

[Setheric]

I get the same error:

seth@home:~/joyce$ cuffmerge -g mm9_refFlat.gtf -s /mm9.fa -p 8 assemblies.txt

[Tue Aug 7 14:58:15 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Aug 7 14:58:15 2012] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/usr/local/bin/cuffmerge", line 576, in <module>
sys.exit(main())
File "/usr/local/bin/cuffmerge", line 546, in main
chrom_info = get_gtf_chrom_info(gtf, chrom_info)
File "/usr/local/bin/cuffmerge", line 476, in get_gtf_chrom_info
left = int(cols[3])
ValueError: invalid literal for int() with base 10: '-'

When I do a similar analysis using the hg19_refFlat.gtf file it runs fine...
Is it a problem with the gtf file?

any help would be greatly appreciated.

Seth

[Setheric]

It must be my refFlat.gtf file because if I rerun the command without the gtf file it works....
I downloaded the hg19 refFlat and mm9 refFlat files from the UCSC Genome Table Browser. They appear similar, any suggestions that may work to modify the mm9 gtf file so it works?

thanks

[jb2]

I'm also getting an issue with running cuffmerge on >250 assemblies. The odd thing is that if I run with only a few assemblies, cuffmerge appears to work fine. It doesn't look like a memory issue either. Anyone have any thoughts on this? Is this fixed potentially in the 2.0.1 or 2.0.2 release of Cufflinks?

Here is the command being run:

cuffmerge -o cuffmerge.output -g Homo_sapiens.GRCh37.64.mod.gtf -p 4 cufflinks.assemblies.txt

[Mon Oct 29 11:47:52 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Mon Oct 29 11:47:52 2012] Preparing output location cuffmerge.lgrc1-18/
Traceback (most recent call last):
File "/share/apps/assembly/Cufflinks/cufflinks-2.0.0_gnu412_x86_64/bin/cuffmerge", line 576, in ? sys.exit(main())
File "/share/apps/assembly/Cufflinks/cufflinks-2.0.0_gnu412_x86_64/bin/cuffmerge", line 546, in main chrom_info = get_gtf_chrom_info(gtf, chrom_info)
File "/share/apps/assembly/Cufflinks/cufflinks-2.0.0_gnu412_x86_64/bin/cuffmerge", line 476, in get_gtf_chrom_info left = int(cols[3])
ValueError: invalid literal for int(): Cufflinks

[adiallo]

Hello, jb2

Did you find a solution to your problem ? I have the same error with 50 GTFs.

Cheers,

Alpha

[yehudithasin]

I just opened a new thread, since the solution here does not work for me

Yehudit

[adiallo]

Hello guys,
There is an error in one of your transcripts generated by cufflinks...
So you can can verify your list by adding files 1 by 1 or rerun all your cufflinks.

Alpha