(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:~$
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