美文网首页
hisat2-align exited with value 1

hisat2-align exited with value 1

作者: vicLeo | 来源:发表于2020-02-20 10:20 被阅读0次
    (rna) lchen@lchen-Vostro-5460:~$ hisat2 -x /home/lchen/reference/hisat2_index/hg38/genome -p 20 -U /home/lchen/circ/sorted/c1.fastq -S /home/lchen/circ/sorted/c1_align.sam
    Error: Encountered one or more spaces while parsing the quality string for read ST-E00494:529:HT3FNCCXY:8:1223:11525:11787.  If this is a FASTQ file with integer (non-ASCII-encoded) qualities, try re-running with the --integer-quals option.
    terminate called after throwing an instance of 'int'
    Aborted (core dumped)
    (ERR): hisat2-align exited with value 134
    (rna) lchen@lchen-Vostro-5460:~$ zgrep -A 4 "ST-E00494:529:HT3FNCCXY:8:1223:11525:11787" /home/lchen/circ/sorted/c1.fastq
    @ST-E00494:529:HT3FNCCXY:8:1223:11525:11787
    TAACAGTGAGGATATTAGGAAGAGGCCAGATCCTATGATTATTTGAAGGTAGGGTAACCAGAATTTGTTATTAGATTGGATGTAGGGTGTGAAGAACAAGGGGGAGGCAAGGATTAGTCCAAGGTTTTATATGTCAGCACCTGAGTGATG
    +
    AAFFFJAJFJJFAJJJJJJJJF<JJJJFJJJJJJJJJFJJJJJJFFJJJJJ<FJJJJJAFJAJAJJJAJFJJFJFJFJ7AFJF<FFFA77AAJJAAJFFJJAAJAJ-7FF<F7FFFJJJJJ<FJAFJA<FJFFJFJFJJFJJJJJ7F7AJ
    @ST-E00494:529:HT3FNCCXY:8:1202:30025:68447
    --
    @ST-E00494:529:HT3FNCCXY:8:1223:11525:11787
    GCCACATCCATATACCTGAAGGTCTAAAATGACACCTACACGTTGGATGAACATATCCAAACAAACATTTTCTTCTCTCCCAAATGCCGCTCCCCTTTCT
    +
                                                                                                        
    @ST-E00494:529:HT3FNCCXY:8:1109:12307:51711
    
    (rna) lchen@lchen-Vostro-5460:~$ echo "`cat /home/lchen/circ/sorted/c1.fastq| wc -l` / (4*1000000)" | bc -l
    50.80315000000000000000
    (rna) lchen@lchen-Vostro-5460:~$ 
    

    相关文章

      网友评论

          本文标题:hisat2-align exited with value 1

          本文链接:https://www.haomeiwen.com/subject/faigfhtx.html