replong error : no ovb files

[ankita86]

Hi, After read correction, I got following error. I tried to troubleshoot as suggested on another thread by reinstalling canu1.4 rather than using 1.7version but cannot figure out the reason for this :

########## Error Message ################# -- Purging correctReads output after merging to final output file. -- Purging disabled by saveReadCorrections=true.

-- Corrected reads saved in '/home/drankitanarang/Desktop/tmp/step1.correctedReads.fasta.gz'. the folder is /home/drankitanarang/Desktop/tmp process reads ls: cannot access correction/1-overlapper/results/*.ovb: No such file or directory

ls: cannot access correction/1-overlapper/results/.ovb: No such file or directory the number of totalfiles is 0 ls: cannot access correction/1-overlapper/results/.ovb: No such file or directory no ovb files merge the bed file cat: *new.bed: No such file or directory 0 use ovl to find overlap

Please help in this regard.

[bzvew]

Hi, can you use the latest code and run replong with "2>&1 | tee replong.log" in the end of your command to record a log file? I update the README file for canu install and fix a canu path issue. You do not need to install canu by yourself now, use .install.sh instead to install canu.

[ankita86]

replong.log Here is log file, as far as I understand it fails after correction.

[bzvew]

Hi, I'm not sure if you use the install.sh to install canu 1.4. I modify some code in Canu, so if you install it by yourself, the behavior can be different. Can you pull the latest code, use install.sh to install canu, then test if replong works?

[ankita86]

Now, I got the error - Fatal error: cannot open file '/home/drankitanarang/replong/linenum.R': No such file or directory though this is not my working directory, processRead.sh is not taking the path directly. How to resolve ?

[bzvew]

Sorry, I update the code today. That issue is a bug. Please use the latest code and try again.

[ankita86]

Ok thanks, please do let me know as soon as you update.