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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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Fatal error in pipeline #7

Closed MathGon closed 9 years ago

MathGon commented 9 years ago

Hi Mac

/home/mgonnet/Soft/mccortex//bin/mccortex31 build  -m 1G -t 2 -k 27 --sample 74_373 --seq2 74_373_1.fastq:74_373_2.fastq out/k27/graphs/74_373.raw.ctx >& out/k27/graphs/74_373.raw.ctx.log
my_job_script.mk:329: recipe for target 'out/k27/graphs/74_373.raw.ctx' failed
make: *** [out/k27/graphs/74_373.raw.ctx] Error 1
make: *** Deleting file 'out/k27/graphs/74_373.raw.ctx'

The end of the corresponding log file that produce the issue is 

05 Aug 2015 19:05:07-vab][hasht]  collisions 15: 10
[05 Aug 2015 19:05:07-vab][hasht]  collisions 16: 6
[05 Aug 2015 19:05:07-vab][hasht]  collisions 17: 6
[src/graph/hash_table.c:311] Error hash_table_find_or_insert_mt(): Hash table is full
[05 Aug 2015 19:05:07-vab] Fatal Error

any idea? Best regards

noporpoise commented 9 years ago

This error means you ran out of memory. When running the pipeline, specify memory with MEM=... e.g.

make -f pipeline.mk MEM=100G

For a human, link information requires high peak memory usage at the moment (~300G). 10 E. coli. samples requires about 2G.

MathGon commented 9 years ago

Thanks, it solves my problem.