Canu error through RepLong: canu failed with 'gatekeeper store exists, but contains no reads'

[LuciaA2]

Hi,

I'm trying to find repeated sequences in the genome of my bacteria through RepLong. When I execute the RepLong command in Linux, it starts to run until the following error appears:

=============================================================
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/carlos/Escritorio/Lucia/replong-master/canu-1.4/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
Traceback (most recent call last):
File "/home/carlos/Escritorio/Lucia/replong-master/edge_1.py", line 87, in
outfilename)
File "/home/carlos/Escritorio/Lucia/replong-master/edge_1.py", line 9, in buildEdgeWithFrom
with open(overlapfile, 'r') as a, open(readlengthfile, 'r') as b,
IOError: [Errno 2] No such file or directory: 'temp/correction/step2.gkpStore/reads.txt'
use community detection to merge repeat
Loading required package: methods

I followed all the instructions on your page, but it seems like the text file doesn't exists

Thank you very much,

Lucía

[bzvew]

Hi, Lucia. Can you find a file called replong.log under your folder when you run replong? I want to check that file.

[LuciaA2]

replong.log

[bzvew]

When you run replong, can you log the running of RepLong to a file for me to check? You can do that by append the "&> test.log" to the command line when you run RepLong. And I want to check that test.log file. You should delete the temp folder of your previous run first. Thanks.

[LuciaA2]

test.log

Thanks.

[bzvew]

Hi, can you find a new.fa file under the folder /home/carlos/Escritorio/Lucia/replong-master/temp/?
If there is, what is the size of that file?

[LuciaA2]

Hi, the temp folder is automatically deleted when after running the script, but the file new.fa is generated in /home/carlos/Escritorio/Lucia/replong-master/. The size of this file is 0 B

[bzvew]

If possible, can you send me the reads1.fasta file for me to test that?

[LuciaA2]

can I send it by mail?.

I have reinstalled Canu but version 1.7 and now other things appear. I attach the file with the text. The first error is on line 567 "llegal division by zero at /home/carlos/Escritorio/REPLONG_nuevo/replong/canu-1.4/Linux-amd64/bin/../lib/site_perl/canu/Gatekeeper.pm line 485 . "

text_canu1.7.log

[bzvew]

Yes, if convenient, please send to [email protected].

[bzvew]

I find it is the file name issue, and your file format is

m160216_153322_42244_c100951122550000001823215806251656_s1_p0/18/0_3761 RQ=0.843

before RQ there is a space, that will cause issue. I remove the RQ field from the input file and the program can run without error. I modify the program to keep new.fa(the file before merging similar reads) and result.fa(the file after merging) in case the result.fa is too small.

[LuciaA2]

Hi,
I have reinstalled everything, with the changes and with my data without spaces and now it returns another error. It's as if it can not find a file (the error is on line 734 of the text.log file):
IOError: [Errno 2] No such file or directory: 'temp/correction/step2.gkpStore/reads.txt'

text.log

[bzvew]

In the log file it shows it is a mix between canu1.4 and canu1.7, and I don't know why it shows canu1.7 when you running canu under the canu1.4 folder. Can you delete the canu-1.4 folder under replong folder, and run ./install.sh again to make sure you only run canu1.4?

[LuciaA2]

I finally got it!. I have changed to version 1.4 of Canu and now it works.

Thank you very much for your help

[jorisbertrand]

Hi,
it looks that I have a quite similar issue but I cannot solve it. Could you help me to try to figure out what happens?
Cheers
test.log