problem with segfaults in splitrim

poeli / GOTTCHA

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problem with segfaults in splitrim #10

Open scholzmb opened 8 years ago

scholzmb commented 8 years ago

I have FINALLY tracked down the issue (or at least identified it) with splitrim segfaulting on my linux system.

somewhere in the D codes, There is a buffer overrun, or filehandle that is being left open, that is causing main to segfault when RETURNING. This means that on my system, splittrim runs, finishes, hangs up for ~20 seconds, then segfaults. I have corrected my local version by runnins splitrim in a system call rather than executeCommand(), but that's not really a good fix. Someone should take a look at splitrim.d and see if they can find the issue.

sb43 commented 8 years ago

Hi @poeli is following splitrim error related to @scholzmb. ----> ENTRY HEADER:@HX4_17986:1:2206:28168:8271 Threads: 1 (effective) 1 (requested) IDX = 0: reading from 0 to 56203948 Staggering at 125000 reads; processed 125000 reads IDX(0) counted 167440 reads GLOBAL READ COUNT = 167440 Trim Time: 900 ms Warning: fault detected in statistics calculation! -> Check either (1) the input ASCII encoding or (2) the # of reads passing filters I am using Illumina 150bp reads, and I did tried splitrim command with correct ASCII encoding. Any help is appreciated.

sb43 commented 8 years ago

worked with lowering the quality filter to 10.