daisyko
commented
4 years ago Hi, may I have your cfg file for FALON_unzip? I tried to run FALCON unzip and got an error of list index out of range error:
File "/my/path/toanaconda3/lib/python3.7/site-packages/falcon_unzip/mains/ovlp_filter_with_phase_strict.py", line 333, in run arid2phase[row[0]] = (row[1], row[2], row[3]) # ctg_id, phase_blk_id, phase_id IndexError: list index out of range
I am thinking whether it is because of missing parameter in the cfg file for FALCON unzip. If you can still find your cfg file, could you please send it out for a reference? Thanks
Hi, I use falcon and get 597 contigs then use falcon_unzip I got 593 contigs in "all_p_ctg.fa". Use 000589F for an example, I found that there has "000589F_ref.fa" bot not "000589F_reads.fa" in 3-unzip/reads/. I also check the "rawread_to_contigs" file in 2-asm-falcon/read_maps/ and "read_to_contig_map" file in 2-asm-falcon/read_maps/get_ctg_read_map/ , found that I really have raw reads can map on 000589F. So I think there is a problem in python -m falcon_kit.mains.rr_ctg_track python -m falcon_kit.mains.pr_ctg_track python -m falcon_kit.mains.fetch_reads I think maybe some of rawreads are shorter than defult(2500). So, I change it like python -m falcon_kit.mains.rr_ctg_track --min_len 300 python -m falcon_kit.mains.pr_ctg_track --min_len 300 python -m falcon_kit.mains.fetch_reads --min_ctg_lenth 1000 But I still can't get 000589F in all_p_ctg.fa. Please help me to solve this problem. Thanks a lot for your help. Sincerely Jeff