SPAdes didn't work
gabrielluishernandez opened this issue · 5 comments
Hello @james-milburn-crowe
I have run into this error while using spades in "part2: genome assembly" practical. I entered the following command:
spades.py -o tmp -1 input/reads.pe1.clean.fq -2 input/reads.pe2.clean.fq
After a few minutes it returned the following and did not create the fasta file:
== Error == system call for: "['/shared/conda/envs/spades/bin/spades-core', '/shared/home/btx645/2021-09-22-assembly/tmp/K33/configs/config.info']" finished abnormally, OS return value: 255
Cheers
I have experienced the identical issue with the same error message. Seems to be a memory allocation issue, see end of log output below:
Command entered:
spades.py -o tmp -1 input/reads.pe1.clean.fq -2 input/reads.pe2.clean.fq
Log From Right before it died:
0:00:00.053 4M / 11M INFO General (kmer_splitters.hpp : 97) Using cell size of 8387114
0:00:08.619 2G / 2G INFO General (kmer_splitters.hpp : 287) Processed 1331909 reads
0:00:08.960 2G / 2G INFO General (kmer_splitters.hpp : 287) Processed 1335418 reads
0:00:09.007 16M / 2G INFO General (kmer_splitters.hpp : 293) Used 1335418 reads
0:00:09.007 16M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:00:09.009 16M / 2G ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12
== Error == system call for: "['/shared/conda/envs/spades/bin/spades-core', '/shared/home/btx452/2021-09-22-assembly/tmp/K33/configs/config.info']" finished abnormally, OS return value: 255
I'd just been looking into this, got the same error - this is to be expected, as we're running with smaller images than the assemblies would be run on - spades takes a large memory footprint. I'm going to mark this as closed, with this as a note - change image size to large when running assembly practical
Hi guys, can you confirm please that this runs with the larger machines? As it could also be a software compatibility issue
Is this resolved?
It ran yesterday properly