Gery_Xu
2021-09-14 23:55
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转录组上游分析之定量比对Hisat2出现内部异常错误

转录组上游分析(Linux)之定量比对Hisat2出现内部异常错误,不知道哪里错了?
如图下:

img

数据用的是trim_galore进行数据过滤的,Hisat2已经构建好索引,1/2指定路径准确,fq.gz文件完整,改SRR1039508根据SRA数据库得知为双端测序,但是一直是这样的错误,不知道怎么回事

另外,我用了fastp进行数据过滤,也得到同样的bug,所以不是数据过滤的问题
同时我把-1和-2的$变量目录改成绝对目录,也是不行,还是同样bug
难道是索引问题?还是Hisat2版本识别不了的问题?
请大家帮忙看一下,是哪里出错了,谢谢大家!

图片转代码服务由CSDN问答提供 功能建议

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mna)033]2tpml1-desktcp:v1p6-/database/genome/Ensembl/Homo.saplens/GRch38release104v1p610:26:17-/database/genome/Ensembl/Homt
   timetorcalltodriverforforwardindex:0:52:04
                                                                                  saplens/GRch8releasel
Homosapiens.GRCh38.104.0Tf3 Homo_sap1ens.GRch38.dna.primary_assembly.genome.3.ht2
                                  ono_sapiens.GRch38.dna.primary_assembly.genome.4.ht2
omosapiens.GRCh38.104.011 ono saplens.GRch38.dnaprimary_assenbly.genome.5.ht2
omo sapiens.GRch38.dna.prinaryassenbly.ta cmosapiens.GRch38.dna.primary_assenbly.genome.6.ht2
Hono sapiens.GRch38.dnu.prmmryassembty.fa.gz cmo.sapiens.GRch38.dna.primary_assenbly.genome.7.ht2
Homo_sapiens.cRchs8.dna.prinary_assembly.genoma.1.ht2
Homosapiens.GRchaa.dna.prinaryassembly.genome.2.ht2
Sinputdr=/hame/vip/groiect/human-64-Asthma-rans/data/cleantata/trim□alorg/
[outdir=/hama/vip6/projct/human-64-Asthma-Trans/Mapping/Hisat/
(rna)033]2:tpml1-desktop:vip6-/database/gonomo/Ensemb1/Hono_sapiens/GRch38_retease104vip6 10:27:49-/database/gomome/Ensembl/Homo_sapiens/GRch38_rolease16
[sindex=/home/vip6/dataoase/genome/Ensembl/Homo_sap1ons/cch38_roleaso10+/Homo_sap1ons.ch3B.ona.primary_assombly.9onome
(rna)033]2:tpmi1-desktop:vip6/database/genoma/Ensembl/Homo_sapiens/GRch38_release104vip610:28:20-/database/gonom/Ensemb/Homo_sapiens/cRch38_rolenso10
[5hisat2-p3-xS{index-1s{inputdirh/sRR1e395e81val1.fq.gz-2s{inputdir]/SRR10395682val_2.fq.qz-Sstcutdir/SRR1039508.Hisataln.sam
Extra parareters]specified:“/home/vip6/database/qenome/Ensenbl/Hono_sapiens/cRch38_release10+/Homosapiens.GRch38.dna.primaryassenbly.genome
also bespecified.Pleaserun HISAT separatelyformntesand singles.
otethatifcmatesfilesarespecifiedusing-1/-2.acsinglesfllecannot
Error:EncounteredintemnalHISAT2exception(#1)
ommand:/home/vip6/miniconoa3/envs/rna/bin/h1sat2-al1on-s--Wrapperbas1c-0-p3-S/hone/v1p6/eroject/human-64-Asthma-Trans/Happing/Hisat//5RR1039508.Hisa
aln.sem·-fead-lengths63.60,59,62.58.57,61,56.51,55,49,54,44,40,52,43.53.50,47,45,39.46,42,37,48,41,38-1/tmp/2713898.inpipe1-2/tmp/2713898.inpipez
 /hone/vip6/database/genone/Ensenbl/Homo_saplens/cRch38_release104/Hono_sapiens.GRch38.dna.prlmary_assembly.gencme
ERR:hisat2-alionexitetwithvalue1
cne03312:tnm-da5k个 中四首
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1条回答 默认 最新

  • Gery_Xu 2021-09-15 00:30

    下面为上图的红圈error信息:

    Extra parameter(s) specified: "/home/vip6/database/genome/Ensembl/Homo_sapiens/GRCh38_release104/Homo_sapiens.GRCh38_release104.genome"
    
    Note that if <mates> files are specified using -1/-2, a <singles> file cannot
    
    also be specified.  Please run HISAT2 separately for mates and singles.
    
    Error: Encountered internal HISAT2 exception (#1)
    
    Command: /home/vip6/miniconda3/envs/rna/bin/hisat2-align-s --wrapper basic-0 -p 3 -S /home/vip6/project/human-64-Asthma-Trans/Mapping/Hisat//SRR1039508.Hisat_aln.sam --read-lengths 63,60,59,62,58,57,61,56,51,55,49,54,44,40,52,43,53,50,47,45,39,46,42,37,48,41,38 -1 /tmp/2597247.inpipe1 -2 /tmp/2597247.inpipe2 ?-x ?/home/vip6/database/genome/Ensembl/Homo_sapiens/GRCh38_release104/Homo_sapiens.GRCh38_release104.genome
    
    (ERR): hisat2-align exited with value 1
    
    
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