I am getting the following error when trying to merge several files produced by cufflinks using output from tophat. I'm using the same reference in both cases and do not know why it would be giving me this error.
Error (GFaSeqGet): end coordinate (121191482) cannot be larger than sequence length 121191424
Error (GFaSeqGet): end coordinate (121191482) cannot be larger than sequence length 121191424
Error (GFaSeqGet): subsequence cannot be larger than 16338
Error getting subseq for CUFF.24532.1 (1..16348)!
[FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
File "/shared/local/cufflinks/cuffmerge", line 573, in ?
sys.exit(main())
File "/shared/local/cufflinks/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/shared/local/cufflinks/cuffmerge", line 406, in compare_meta_asm_against_ref
tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
File "/shared/local/cufflinks/cuffmerge", line 342, in compare_to_reference
exit(1)
TypeError: 'str' object is not callable
If anyone knows why this is happening or how to circumvent it, that would be great.
Error (GFaSeqGet): end coordinate (121191482) cannot be larger than sequence length 121191424
Error (GFaSeqGet): end coordinate (121191482) cannot be larger than sequence length 121191424
Error (GFaSeqGet): subsequence cannot be larger than 16338
Error getting subseq for CUFF.24532.1 (1..16348)!
[FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
File "/shared/local/cufflinks/cuffmerge", line 573, in ?
sys.exit(main())
File "/shared/local/cufflinks/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/shared/local/cufflinks/cuffmerge", line 406, in compare_meta_asm_against_ref
tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
File "/shared/local/cufflinks/cuffmerge", line 342, in compare_to_reference
exit(1)
TypeError: 'str' object is not callable
If anyone knows why this is happening or how to circumvent it, that would be great.
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