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:mag: Post Assembly Variants Finder
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Fusion-bloom reporting "TypeError" #15

Closed Rohanbha closed 3 years ago

Rohanbha commented 3 years ago

Hello, I have run "fusion-bloom" script on multiple samples using the following command -

fusion-bloom profile=fusion_profile_chickpea.txt left=SRR12081280/reads/SRR12081280_1_trim.fastq right=SRR12081280/reads/SRR12081280_2_trim.fastq readlen=125 outdir=SRR12081280/SRR12081280_FusionBloomOut name=chickfus

I got results from some samples which are smaller in size (<2GB), but the script terminates for larger runs reporting an error -

"Traceback (most recent call last): File "/home/nipgr/software/pavfinder_env/bin/find_sv_transcriptome.py", line 259, in main() File "/home/nipgr/software/pavfinder_env/bin/find_sv_transcriptome.py", line 226, in main only_fusions=args.only_fusions File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/sv_finder.py", line 297, in find_events events.extend(process_split_aligns([align1, align2], query_seq, genes)) File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/sv_finder.py", line 158, in process_split_aligns self.update_adj(adj, aligns, query_seq, target_type, block_matches=block_matches) File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/sv_finder.py", line 723, in update_adj self.is_fusion(adj, (aligns[0].strand, aligns[1].strand), target_type) File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/sv_finder.py", line 1664, in is_fusion self.is_sense_fusion(adj, align_strands, target_type) File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/sv_finder.py", line 1719, in is_sense_fusion within_utrs = (adj.transcripts[0].within_utr(adj.genome_breaks[0]), File "/home/nipgr/software/pavfinder_env/lib/python3.6/site-packages/pavfinder/transcriptome/transcript.py", line 351, in within_utr if pos >= utr5[0] and pos <= utr5[1]: TypeError: '>=' not supported between instances of 'NoneType' and 'int'"

Please help me out with this issue.

readmanchiu commented 3 years ago

Sorry @Rohanbha I glossed over this in my mailbox and apologized for the late reply. I will fix this bug and update when it is done.

readmanchiu commented 3 years ago

Hi @Rohanbha,

Please try running again hopefully the bug is fixed.