Cuffmerge command giving error- TypeError: 'str' object is not callable

[kumardeep]

Hi all
I am merging the 1 test sample transcripts.gtf and 1 control sample transcripts.gtf files through cuffmerge via this command :

cufflinks-2.0.0.Linux_x86_64/cuffmerge -s ref-genomes/hg19.fa assemblies.txt

where hg19.fa is reference genome which I used to align the raw reads. I am not giving reference GTF file for the moment.
assemblies.txt contains 2 lines:
/home/kumardeep/ngs/control/transcripts.gtf
/home/kumardeep/ngs/test/transcripts.gtf

The error i am getting is as :
[Fri May 11 10:09:51 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Fri May 11 10:09:51 2012] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Fri May 11 10:09:54 2012] Converting GTF files to SAM
Traceback (most recent call last):
File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 576, in ?
sys.exit(main())
File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 554, in main
sam_input_files = convert_gtf_to_sam(gtf_input_files)
File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 287, in convert_gtf_to_sam
sam_out = gtf_to_sam(line)
File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 252, in gtf_to_sam
exit(1)
TypeError: 'str' object is not callable


Please suggest the useful
Thanks
Kumardeep

[davidblaney]

Hi Kumardeep,

Could it be that you left out gtf_to_sam from you PATH?

the code looks light it might be something to do with this.

David