dstreett
Odd behavior
I'm noticing odd behavior while playing around with -m and -M. The program just dies with output stopping and returning me to a command prompt. The last output being Read_Offset.
The command line that I was using: $flash2 -m 65 -M 300 reads_R1.fastq reads_R2.fastq 2>&1 | tee flash.log
The behavior isn't easy to replicate. I found that, when it does happen, if I just keep rerunning the program it eventually completes.
Trying again with this command Flash version info FLASH v2.2.00 Copyright (C) 2012 Tanja Magoc Copyright (C) 2012, 2013, 2014 Eric Biggers Modifications 2015 David Streett License GPLv3+; GNU GPL version 3 or later http://gnu.org/licenses/gpl.html. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.
$flash2 --max-overlap 600 --allow-outies -t 30 -C 70 -Q 20 output_nodup_PE1.fastq output_nodup_PE2.fasttq &> flash.log Segmentation fault
Is -o required?
I think my previous errors were segFaults. When I used '2>&1' it blocked the stderr of segFault. When I ran the same line above a second time I got another segFault. When I ran it a third time, without '&>' the program ran and output was standard.
I'm going to compile my own version and see if that fixes the problem. If not, I'm going to recompile with -g -traceback and start narrowing down possibilities.