canu failed with 'gatekeeper store exists, but contains no reads'.

[maoying0423]

Hi, I tried to run the human_100k.fa file in Replong to find the repeat sequence, but the following problem

Don't panic, but a mostly harmless error occurred and canu failed.

canu failed with 'gatekeeper store exists, but contains no reads'.

temp/correction/1-overlapper/001/.ovb ERROR: invalid arg 'temp/correction/1-overlapper/001/.ovb' usage: /home/maoying/software/canu/replong/canu/Linux-amd64/bin/overlapConvert [options] file.ovb[.gz]

-G gkpStore (needed for -coords, the default)

-coords output coordiantes on reads -hangs output hangs on reads -raw output raw hangs on reads

-native input ovb file is NOT snappy compressed

ERROR: no overlap files supplied filter overlap file to merge repeat ovlfile is: all.ovl lengthfile is: temp/correction/step2.gkpStore/reads.txt fromlength is: 250 lendiff is: 200 ratio is: 0.96 output_edge is: new.edge Traceback (most recent call last): File "/home/maoying/software/canu/replong/edge_1.py", line 93, in outfilename) File "/home/maoying/software/canu/replong/edge_1.py", line 9, in buildEdgeWithFrom with open(overlapfile, 'r') as a, open(readlengthfile, 'r') as b,\ FileNotFoundError: [Errno 2] No such file or directory: 'temp/correction/step2.gkpStore/reads.txt' use community detection to merge repeat

载入程辑包：‘igraph’

The following objects are masked from ‘package:stats’:

decompose, spectrum

The following object is masked from ‘package:base’:

union

Error in file(file, "rt") : 无法打开链结 Calls: read.table -> file 此外: Warning message: In file(file, "rt") : 无法打开文件'new.edge': 没有那个文件或目录 停止执行 split: 无法打开'new.line' 读取数据: 没有那个文件或目录 ls: 无法访问'new*.line': 没有那个文件或目录 ls: 无法访问'new.sed': 没有那个文件或目录 ls: 无法访问'new_.bed': 没有那个文件或目录 ls: 无法访问'new_sorted.bed': 没有那个文件或目录 Find original read names cat: 'new.name': 没有那个文件或目录 cat: 'new_*_sorted.bed': 没有那个文件或目录 extract repeat sequences Traceback (most recent call last): File "/home/maoying/miniconda3/bin//faidx", line 8, in sys.exit(main()) File "/home/maoying/miniconda3/lib/python3.7/site-packages/pyfaidx/cli.py", line 168, in main write_sequence(args) File "/home/maoying/miniconda3/lib/python3.7/site-packages/pyfaidx/cli.py", line 16, in write_sequence fasta = Fasta(args.fasta, default_seq=args.default_seq, strict_bounds=not args.lazy, split_char=args.delimiter, filt_function=filt_function) File "/home/maoying/miniconda3/lib/python3.7/site-packages/pyfaidx/init.py", line 658, in init sequence_always_upper=sequence_always_upper) File "/home/maoying/miniconda3/lib/python3.7/site-packages/pyfaidx/init.py", line 306, in init self.build_index() File "/home/maoying/miniconda3/lib/python3.7/site-packages/pyfaidx/init.py", line 399, in build_index valid_entry = check_bad_lines(rname, bad_lines, i) # advance index since we're at the end of the file UnboundLocalError: local variable 'i' referenced before assignment the file before merging is new.fa the result file name is result.fa I followed all the instructions on your page, but the problem seems to have arisen anyway Thank you very much

[maoying0423]

This is the test.log generated at runtime test.log

[ruiguo-bio]

Hello. Thank you for reporting that. I fix that issue caused by awk version and please pull the new code, and you can run your old command again in the same folder to reduce the computing time for canu.

[maoying0423]

Thank you very much for your help