Program errors with laconic message
jakobnissen opened this issue · comments
I'm running MetaMDBG and get the following output to stderr as the program errors:
Input: sample1/tmp//input.txt
Dir: sample1
Minimizer length: 13
Density: 0.005
Checking dependencies: bgzip (wfmash package) ok
Checking dependencies: samtools ok
Checking dependencies: wfmash ok
Checking dependencies: minimap2 ok
Converting reads to minimizers...
N50 read length: 8058
Min k: 4
Max k: 80
Multi-k pass: 4/80
ERROR (logs: sample1/tmp//logs.txt)
I've attached the logs.txt (but note I had to manually copy-paste it to get it out of our cluster, so some of the lines where it just says the number of reads processed is replaces with [etc])
The input is a 47 GB gzip compressed FASTQ file, and the program is run with 80 GB RAM.
It's possible this is an out of memory-error, so I've rerun it with 1500 GB RAM, however, in that case, the error message is less than perfect.
This is metaMDBG 0.3 running on Linux.
Yes it's probably an out of memory exception. I will try to improve the error messages.