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GATB / gatb-minia-pipeline

GATB Minia assembly pipeline
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920: syntax error in expression (error token is "920") #23

Closed osowiecki closed 4 years ago

osowiecki commented 4 years ago

(2019-12-24 19:56:17) Minia assembling at k=21 min_abundance=2 (2019-12-24 19:56:17) Execution of 'minia/minia'. Command line: /NGStools/gatb-minia-pipeline/tools/memused /NGStools/gatb-minia-pipeline/minia/minia -in assembly.list_reads -kmer-size 21 -abundance-min 2 -out assembly_k21 Minia 3, git commit 40f35ad setting storage type to hdf5 [Approximating frequencies of minimizers ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 22, 22, 22] MB /NGStools/gatb-minia-pipeline/tools/memused: line 13: 22872 920: syntax error in expression (error token is "920") [Approximating frequencies of minimizers ] 100 % elapsed: 0 min 29 sec remaining: 0 min 0 sec cpu: 93.9 % mem: [ 22, 22, 22] MB [DSK: Pass 1/1, Step 1: partitioning ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 76, 76, 91] MB

rchikhi commented 4 years ago

Thanks for the report! It's an inconsequential bug in the memused script that reports memory usage. I'm having trouble reproducing it on small datasets. Probably won't fix. (unless someone suggests a fix in that script..)