Closed Lixx1989 closed 5 months ago
skoren
commented
7 months ago The first two errors are due to the same issue I suspect. The last one looks different but might be related if the out-of-bounds array access corrupted something else. Are you able to share the ctgStore and the seqStore for this assembly?
Lixx1989
commented
7 months ago The size ctgStore and the seqStore are about 16G and 26G. Should I send them as email attachments?
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Sergey ***@***.***>
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11/17/2023 00:08
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Re: [marbl/canu] Canu v2.3 Failed with 'Segmentation fault'; backtrace (libbacktrace) (Issue #2276)The first two errors are due to the same issue I suspect. The last one looks different but might be related if the out-of-bounds array access corrupted something else. Are you able to share the ctgStore and the seqStore for this assembly?
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skoren
commented
7 months ago You can upload them to our FTP following the instructions here: https://canu.readthedocs.io/en/latest/faq.html#how-can-i-send-data-to-you
Lixx1989
commented
7 months ago I have tried put ctgStore and seqStore to ftp.cbcb.umd.edu/incoming/sergek with ftp of linux. The file is too large for interactive connection. And it always showed ' 421 Data timeout'. Then I tried it using nohup of shell. However, sergek could not create file. The followings are my script and error message.---script----nohup ftp -ivn ftp.cbcb.umd.edu < ftp_put.txt---ftp_put.txt----user anonymous 123456binary cd incoming/sergek put bx_canu.seqStore.tar.gz bye --error message---Connected to ftp.cbcb.umd.edu. 220- 220-Welcome to the CBCB FTP Server 220- 220-Please visit, http://www.cbcb.umd.edu 220-for more information. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. local: bx_canu.seqStore.tar.gz remote: bx_canu.seqStore.tar.gz 200 PORT command successful. Consider using PASV. 553 Could not create file. 221 Goodbye.
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Sergey ***@***.***>
Date
11/22/2023 05:28
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Re: [marbl/canu] Canu v2.3 Failed with 'Segmentation fault'; backtrace (libbacktrace) (Issue #2276)You can upload them to our FTP following the instructions here: https://canu.readthedocs.io/en/latest/faq.html#how-can-i-send-data-to-you
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skoren
commented
7 months ago The FTP doesn't let you upload files w/duplicate file names so once your initial upload failed, there was a truncated tar.gz that blocked subsequent uploads unless you renamed them. I renamed your partial uploads so you can try again. We've definitely uploaded larger files than yours using interactive or command-line ftp. If you keep having dropped connections, can you share in another way, for example google drive or similar?
skoren
commented
5 months ago Idle, no data to reproduce. Might have been fixed by a recent commit to utgcns.
Hi, I repeatedly encountered this error and I don't seem to be able to pinpoint the problem. I'm running canu on a linux grid, with 1 node, 128 cores, and enough storage space left. My assembly is about 1.5g.
--Command-- /media/disk1/software/canu/build/bin/canu -p bx_canu -d assembly genomeSize=1.5g useGrid=false --pacbio-hifi /media/disk1/xxli/hifi/CRR783774.fq.gz --Version-- canu snapshot v2.3-development +139 changes (r10410 a55ecfaa3fa1d39ba7d0a577dcc5e4cd6c413ca0)
About four consensus jobs failed. I am pasting the error message from of 3 consensus files (consensus.000010.out and ). And they are different error messages.