megahit 返回0结果

最新推荐文章于 2023-09-01 16:30:35 发布

Hakuna_mata_ta_

最新推荐文章于 2023-09-01 16:30:35 发布

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分类专栏：随手记

本文链接：https://blog.csdn.net/hakuna_mata_ta_/article/details/108828257

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在使用megahit进行基因组组装时遇到返回0结果的问题，尝试通过重新下载序列、配置docker环境、解压文件及调整参数来解决，但运行后依然报错。log.txt显示scanning进程异常。同时，尝试使用SPAdes和khmer也报错。检查官方文档未找到直接解决方案，问题待解决。

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base) yuanchao@habri323:~/megahit/assembly$ time megahit -t 8 --k-min 29 --k-max 171 --k-step 20  SRR1976948.abundtrim.subset.pe.fq.gz,SRR1977249.abundtrim.subset.pe.fq.gz-o out
2020-09-27 14:57:16 - MEGAHIT v1.2.9
2020-09-27 14:57:16 - Maximum number of available CPU thread is 2.
2020-09-27 14:57:16 - Number of thread is reset to the 2.
2020-09-27 14:57:16 - Using megahit_core without POPCNT and BMI2 support, because the features not detected by CPUID 
2020-09-27 14:57:16 - Convert reads to binary library
2020-09-27 14:57:16 - b'INFO  utils/utils.h                 :  152 - Real: 0.0002\tuser: 0.0000\tsys: 0.0031\tmaxrss: 7228'
2020-09-27 14:57:16 - Start assembly. Number of CPU threads 2 
2020-09-27 14:57:16 - k list: 29,49,69,89,109,129,149,169,171 
2020-09-27 14:57:16 - Memory used: 1842823987
2020-09-27 14:57:16 - Extract solid (k+1)-mers for k = 29 
2020-09-27 14:57:16 - Build graph for k = 29 
2020-09-27 14:57:17 - Assemble contigs from SdBG for k = 29
2020-09-27 14:57:17 - Local assembly for k = 29
2020-09-27 14:57:17 - Extract iterative edges from k = 29 to 49 
2020-09-27 14:57:17 - Merging to output final contigs 
2020-09-27 14:57:17 - 0 contigs, total 0 bp, min 0 bp, max 0 bp, avg 0 bp, N50 0 bp
2020-09-27 14:57:17 - ALL DONE. Time elapsed: 0.837216 seconds

发现是序列没下载完整，重新配置megahit环境（用docker），下载并解压*.pe.fq.gz文件，设置参数，重新运行，如下：

out  SRR1976948.abundtrim.subset.pe.fq  SRR1977249.abundtrim.subset.pe.fq
(megahit) yuanchao@habri323:~/megahit$ time megahit -t 2 --k-min 29 --k-max 171 --k-step 20 -1 SRR1976948.abundtrim.subset.pe.fq -2 SRR1977249.abundtrim.subset.pe.fq -o jjj
2020-09-27 16:53:12 - MEGAHIT v1.2.9
2020-09-27 16:53:12 - Using megahit_core without POPCNT and BMI2 support, because the features not detected by CPUID 
2020-09-27 16:53:12 - Convert reads to binary library
2020-09-27 16:53:37 - b'INFO  sequence/io/sequence_lib.cpp  :   77 - Lib 0 (/home/yuanchao/megahit/SRR1976948.abundtrim.subset.pe.fq,/home/yuanchao/megahit/SRR1977249.abundtrim.subset.pe.fq): pe, 5852308 reads, 251 max length'
2020-09-27 16:53:37 - b'INFO  utils/utils.h                 :  152 - Real: 25.5522\tuser: 12.5292\tsys: 4.0063\tmaxrss: 240620'
2020-09-27 16:53:38 - Start assembly. Number of CPU threads 2 
2020-09-27 16:53:38 - k list: 29,49,69,89,109<