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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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exit code 1 : unrecognized option '--bubble_level' with --presets meta-large #145

Closed aparada closed 6 years ago

aparada commented 6 years ago

Hello, I am getting the an 'exit code 1' error when trying to assemble some metagenomes, and the log appears to indicates 'assemble: unrecognized option '--bubble_level' uknown option'

Below is the command I used, and the error. I've also attached the log file. I should also note that I get the same error without the -m parameter. Any suggestions?

megahit -1 4LO_forward_paired_5_subsampled.fastq.gz -2 4LO_reverse_paired_5_subsampled.fastq.gz -o megahit_4LO_5 --presets meta-large -t 50 -m 0.5

1007.0Gb memory in total. Using: 503.933Gb. MEGAHIT v1.0.3-29-g707d683 --- [Sun Nov 19 11:48:52 2017] Start assembly. Number of CPU threads 50 --- --- [Sun Nov 19 11:48:52 2017] Available memory: 1082187350016, used: 541093675008 --- [Sun Nov 19 11:48:52 2017] Converting reads to binaries --- [read_lib_functions-inl.h : 209] Lib 0 (4LO_forward_paired_5_subsampled.fastq.gz,4LO_reverse_paired_5_subsampled.fastq.gz): pe, 5362132 reads, 150 max length [utils.h : 124] Real: 7.5402 user: 5.7990 sys: 0.8520 maxrss: 165156 --- [Sun Nov 19 11:48:59 2017] k list: 27,37,47,57,67,77,87,97,107,117,127 --- --- [Sun Nov 19 11:48:59 2017] Extracting solid (k+1)-mers and building sdbg for k = 27 --- --- [Sun Nov 19 11:49:50 2017] Assembling contigs from SdBG for k = 27 --- Error occurs when assembling contigs for k = 27, please refer to megahit_4LO_5/log for detail [Exit code 1]

Log: megahit.log

voutcn commented 6 years ago

Please use the latest version v1.1.2.