First thanks for provide such a good tool for circRNA study. Now I am trying to using CIRC2 to do the circRNA alternative splicing detecting. When I follow the manual in the "denovo" step, I got a error below:
Traceback (most recent call last):
File "/home/tongwei/miniconda3/bin/CIRCexplorer2", line 11, in sys.exit(main())
File "python3.6/site-packages/circ2/command_parse.py", line 59, in main command=command_log, name='denovo')
File "python3.6/site-packages/circ2/helper.py", line 38, in wrapper fn(*args)
File "python3.6/site-packages/circ2/denovo.py", line 70, in denovo annotate_fusion(ref_path, options['--bed'], denovo_flag=1)
File "python3.6/site-packages/circ2/annotate.py", line 47, in annotate_fusion genes, novel_genes, gene_info, chrom_info = parse_ref(ref_f, 1)
File "python3.6/site-packages/circ2/parser.py", line 75, in parse_ref starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
File "python3.6/site-packages/circ2/parser.py", line 75, in starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
ValueError: invalid literal for int() with base 10: '"XXXXXXXXXX(gene_id)"'
The command is: CIRCexplorer2 denovo -r gtf -g ref.fa --as=AS --abs=ABS -b STAR_fusion_junction.bed --rpkm --no-fix > CIRCexplorer2_denovo.log
kepbod
commented
6 years ago 
tw7649116
Dear CIRCexplorer2 team,
First thanks for provide such a good tool for circRNA study. Now I am trying to using CIRC2 to do the circRNA alternative splicing detecting. When I follow the manual in the "denovo" step, I got a error below:
Traceback (most recent call last): File "/home/tongwei/miniconda3/bin/CIRCexplorer2", line 11, in sys.exit(main())
File "python3.6/site-packages/circ2/command_parse.py", line 59, in main command=command_log, name='denovo')
File "python3.6/site-packages/circ2/helper.py", line 38, in wrapper fn(*args)
File "python3.6/site-packages/circ2/denovo.py", line 70, in denovo annotate_fusion(ref_path, options['--bed'], denovo_flag=1)
File "python3.6/site-packages/circ2/annotate.py", line 47, in annotate_fusion genes, novel_genes, gene_info, chrom_info = parse_ref(ref_f, 1)
File "python3.6/site-packages/circ2/parser.py", line 75, in parse_ref starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
File "python3.6/site-packages/circ2/parser.py", line 75, in starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
ValueError: invalid literal for int() with base 10: '"XXXXXXXXXX(gene_id)"'
The command is: CIRCexplorer2 denovo -r gtf -g ref.fa --as=AS --abs=ABS -b STAR_fusion_junction.bed --rpkm --no-fix > CIRCexplorer2_denovo.log
The GTF file is like this: xpSc0053480 XX exon 128880 128963 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "1" exon_id "CSA022660.1.1" xpSc0053480 XX exon 129316 129384 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "2" exon_id "CSA022660.1.2" xpSc0053480 XX exon 129475 129540 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "3" exon_id "CSA022660.1.3" xpSc0053480 XX exon 129677 129847 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "4" exon_id "CSA022660.1.4" xpSc0053480 XX exon 129929 130278 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "5" exon_id "CSA022660.1.5" xpSc0053480 XX exon 131060 131340 . - . gene_id "CSA022660" transcript_id "CSA022660.1" exon_number "6" exon_id "CSA022660.1.6"
What may caused this error? Thanks for the help.