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Usage on Mac - megahit_core read2sdbg #346

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feeka opened this issue Jan 3, 2023 · 0 comments
Open

Usage on Mac - megahit_core read2sdbg #346

feeka opened this issue Jan 3, 2023 · 0 comments

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@feeka
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feeka commented Jan 3, 2023

I tried executing the read2sdbg on Mac (2.3 Quad-Core intel i5 w 16Gb RAM), but seems like the execution did not go through:

IN>> megahit_core read2sdbg --read_lib_file ERR3426146.fastq --o out --host_mem 0.9                
------------------------------------------------------------------------------------------------   
INFO  sorting/base_engine.cpp       :  148 - Preparing data...
INFO  sequence/io/sequence_lib.cpp  :  115 - Before reading, sizeof seq_package: 1649267441876
INFO  sequence/io/sequence_lib.cpp  :  117 - After reading, sizeof seq_package: 1649267441876
INFO  sorting/read_to_sdbg_s1.cpp   :  105 - 0 reads, 0 max read length, 0 total bases
INFO  sorting/read_to_sdbg_s1.cpp   :  109 - 2 words per substring
INFO  sorting/read_to_sdbg_s1.cpp   :  124 - Number of files for mercy candidate reads: 1
INFO  sorting/base_engine.cpp       :  153 - Preparing data... Done. Time elapsed: 0.0053
INFO  sorting/base_engine.cpp       :  156 - Preparing partitions and calculating bucket sizes...
zsh: killed     megahit_core read2sdbg --read_lib_file ERR3426146.fastq --o out --host_mem 0.

Unfortunately I have no idea what is happening and how to continue... Is there any manual on specifically sdbg builder?

Best regards,
Fikrat

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