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Old 04-22-2017, 03:59 AM   #1
elaJS
Junior Member
 
Location: Harpenden

Join Date: Apr 2017
Posts: 1
Default cuffmerge errors

Hi,

While running cuffmerge I am facing the following error:
Traceback (most recent call last):
File "/software/cufflinks-2.2.1/cuffmerge", line 580, in ?
sys.exit(main())
File "/software/cufflinks-2.2.1/cuffmerge", line 554, in main
sam_input_files = convert_gtf_to_sam(gtf_input_files)
File "/software/cufflinks-2.2.1/cuffmerge", line 287, in convert_gtf_to_sam
sam_out = gtf_to_sam(line)
File "/software/cufflinks-2.2.1/cuffmerge", line 252, in gtf_to_sam
exit(1)
TypeError: 'str' object is not callable


I used the following command:
bsub -m tarrcwn4 -R"rusage[mem=3000]" -o merge_time1.log.out '/software/cufflinks-2.2.1/cuffmerge -p 1 -o MERGED -g /shared/live/000_rawData/001_HBdata/Hbgenome.gtf -s /shared/live/001_rootTranscripts/004_RNAseq/hb_genome.fa assembly_gtf.txt'

I must say I have done mapping with STAR and then use samtools, cufflinks to generate transcripts.gtf files. The paths to transcripts.gtf files are in assembly_gtf.txt

Thanks in advance for your help
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