Hey all,
I've recently installed maq on my laptop (running ubuntu 9.04 64-bit) and was able to get it up and running with no problem. I ran the following command and it created the appropriate output:
Since maq was a little too much for my laptop to handle, I decided to have my Department's systems administrator install maq on our high performance computing cluster so that I could submit batch jobs to the cluster (using platform LSF). After about 30 seconds a segmentation fault occurs every time using the same command I successfully used on my laptop. It seems to happen right after maq sets the read length and before it loads the reads. Our systems administrator tried to roll back to an older version of maq (6.something) he still got the same problem. This is the email I got from LSF after the cluster tried to run the code and failed.
Is anyone else having this problem? Any guesses why it would work on my computer but not on LSF? We used the same exact binaries to install the files! Thanks so much!
I've recently installed maq on my laptop (running ubuntu 9.04 64-bit) and was able to get it up and running with no problem. I ran the following command and it created the appropriate output:
Code:
maq match test.map refchrom/chr22.bfa FAIRE_data/GM12878/UNCsequencing/raw_data/Rep2/s_2_sequence.bfq
Code:
Job <maq match test.map refchrom/chr22.bfa FAIRE_data/GM12878/UNCsequencing/raw_data/Rep2/s_2_sequence.bfq> was submitted from host <diamond.bios.unc.edu> by user <nrashid>. Job was executed on host(s) <andesite.bios.unc.edu>, in queue <bat>, as user <nrashid>. </home/users/nrashid> was used as the home directory. </home/users/nrashid> was used as the working directory. Started at Tue Feb 10 17:02:21 2009 Results reported at Tue Feb 10 17:03:33 2009 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input maq match test.map refchrom/chr22.bfa FAIRE_data/GM12878/UNCsequencing/raw_data/Rep2/s_2_sequence.bfq ------------------------------------------------------------ Exited with exit code 139. Resource usage summary: CPU time : 20.09 sec. Max Memory : 1915 MB Max Swap : 2850 MB Max Processes : 3 Max Threads : 3 [B] The output (if any) follows: -- maq-0.7.1 [ma_load_reads] loading reads... [ma_load_reads] set length of the first read as 35. /home/users/nrashid/.lsbatch/1234303339.152072: line 8: 29828 Segmentation fault (core dumped) maq match test.map refchrom/chr22.bfa FAIRE_data/GM12878/UNCsequencing/raw_data/Rep2/s_2_sequence.bfq[/B]
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