#19 sh: line 1: 4952 Segmentation fault: 11

[Karsten Liere]

Hi,

lately I'm getting this error with A5 (with both, the 201406 and 201411 versions). After this a crash log for idba_ud500 is written and A5 tries to go ahead with: "[a5] Previous IDBA-UD run failed. Trying again single-threaded".

However, this will ultimately fail with this error: "Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
a5] Error in detecting misassemblies."

Interestingly, this error occurs as well on OS X 10.9.5 as on 10.10.4.

I'm kind of puzzled since I've already successfully assembled much bigger data sets with A5.

Thanks for any input :-)

Cheers,

Karsten

[Karsten Liere]

Hi,

well I tried the latest A5 version 20150522, however, IDBA is still crashing, both 4- ("sh: line 1: 4930 Segmentation fault: 11") and single-threaded ("sh: line 1: 5031 Segmentation fault: 11"). A5 finally aborts with this message: "Modification of non-creatable array value attempted, subscript -1 at /Applications/Apps/Science/NGS/Assembler/A5/bin/a5_pipeline.pl line 832, <FASTQ> line 3305."

[hmontenegro]

I was getting these same errors as well, but in the end it turned out I was inputing the forward reads file twice. Are you sure you are not doing the same?
edit: in any case, I was getting an assembly at he end, even with the errors.