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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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assembly graph #93

Closed heziqing closed 3 years ago

heziqing commented 3 years ago

Dear Dr. Hu， Describe the bug I want to use the assembly graph to run SALSA ( A tool to scaffold long read assemblies with Hi-C), so I change the nextgraph_options= -a 3, not -a 1. But I meet an error, as follows. I had run the nextDenovo successfully before with the nextgraph_options= -a 1 before.

Error message Traceback (most recent call last): File "/share/home/heziqing/NextDenovo2.3.1/nextDenovo", line 783, in main(args) File "/share/home/heziqing/NextDenovo2.3.1/nextDenovo", line 754, in main asm, stat = gather_ctg_cns_output(cfg, task.subtasks, seq_info) File "/share/home/heziqing/NextDenovo2.3.1/nextDenovo", line 278, in gather_ctg_cns_output out = cal_n50_info(stat, asm + '.stat') File "/share/home/heziqing/NextDenovo2.3.1/lib/kit.py", line 171, in cal_n50_info out += "%-5s %18d%20s\n" % ("Min.", stat[-1], '-') IndexError: list index out of range

thanks in advance!

moold commented 3 years ago

Hi, NextDenovo does not support outputting the final result in GFA2 format, while it can output the intermediate result in GFA2 format. You can change to 03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0 directory, and run -a 1 to get fasta file and run -a 3 to get GFA2 file. This result file has some differences with the final result and may contain more errors.

heziqing commented 3 years ago

ok, thanks!