bug (?): non standard FATQ file on paired read about fastp

[sfchen]

I am able to reproduce this error, fixing it soon, thanks!

[sfchen]

The error was caused by that the quality line is started with @, and then it's recognised as sequence name.

I have fixed it and released v0.6.1 with this bug fix. Please try again.

[sfchen]

@Toliman06 could you update this issue once you've tried new fastp release?

[Toliman06]

@sfchen Hi. I installed the new fastp version on my subsamples. The bug is fixed.
I will run the alignment tool after and keep you in touch if everything is fine.
I love your tool and I have few question:

• when using the -W and -M options, is it possible to disable the -q, -u and -n options? I tried a -W -M -Q line, but all the options were disables, including the -W and -Q... (I want to use per the "read cutting by quality options" and disable the "quality filtering options" in the same time)

Here is the new form of my fastq file:

ffcf607a-7b70-4e16-a60b-c09197fa1601_1Mreadshead_windows_W20M30_2.fastq.gz.100lines.fastq

@HWI-1KL150:70:C74KBACXX:1:1101:1931:1994 2:N:0:ATGCCT ACAGCCTGCGGGGGGAATGTGACCAGGATATGCCTCAGCGTCCCAAGAGCGCTTACATGAGTGGGAGTTTGCCCCAACCCCGGGCTGAGGGCCAGAGCGGC + @CCFFFFFHGHHGID9@BCDEDDDDDBBCCC@@C@CDDABDDDBDDDD?90:BDDCDECDD@A?BDD<CCDCDABB@BDDDDBB>9>BDDDDD<B?<CBD9 @HWI-1KL150:70:C74KBACXX:1:1101:4185:1976 2:N:0:ATGCCT ACACTAGCCACTCACGTTCCATCTCTTCCTCGGAGAAATCCTCAGGCCCAGCCAAGGGCAGGAGCAAAAAGGGGAGAATGTCCACCTCAGGTCCAAGCAAC + CCCFFFFFHHHHHJJJHIIJJJIJJJJJJIJJIJJJJJJIJJJJJJIIJJFHIJIJJJIIHHGFFFFDDDDDDD@BBDDDDDDDDDDDDDD@CDD>CBBDA @HWI-1KL150:70:C74KBACXX:1:1101:4438:1971 2:N:0:ATGCCT GTTTGGAGAACCTGTGTGAAAATCCATACTTTAGCAATCTAAGGCAAAACATGAAAGACCTTATCCTACTTTTGGCCACAGTAGCTTCCAGTGTGCCGAAC + CCCFFFFFHHHHHJJJHIJJJJJJJIJJJIJJIJIJJJJJIIIIJJIJIIDDEIGGHJHGGGIIIGGDGHIJJJHHHHFFFCDECCCEECDCCDCCCD??3 @HWI-1KL150:70:C74KBACXX:1:1101:4539:1970 2:N:0:ATGCCT GGCCTCGTGCGCTCGGGCCCGCACGCCGTTGTTCGCGTCACCCCCACCCAGCTCCCTTCCGCGTGTGCTCGGAGGGCGCGGCGCACCGCCTACGCAGGCCN + CCCFFFFFHHHHHJJJJIJJJJJJJJJJIJHEHHFFDDBDDDDDDDDDDDDDDDDDDDDDDDDBDBDDDCDD;BBDDDDDDBD@BDDDD<<>CDDBBDDD> @HWI-1KL150:70:C74KBACXX:1:1101:4702:1995 2:N:0:ATGCCT CAAGCAGCGGCTTTTCCCTGCAGGATCCGCGTAGGCTGCCACAAGCTCATCAACCACCACATCTTCACCAACCTCATCCTTGTCTTCATCATGCTGAGCAN + CCCFFFFFHHHHHJJJIIIIJIJJJIJJIJJEHEIIIIDGHIGIAEHHHH?@DEFFDDDDDCDCDEDDD>B@BCDCCDDACDCDDDDEEE@CDDCCCBDD3 @HWI-1KL150:70:C74KBACXX:1:1101:6121:1971 2:N:0:ATGCCT AGACAGGAGACTCTATAAGAATTTATGAGGCAGCAGAGTCTACAAGTAAATCATGAATCCAGTTGAAAATGTTAATGAGGCCATAGACGTGGTGAAGGATT + @C@DFFFFHHHGHJJJJIIIHIIJJJJIGIJJJJIIIJGHIJIIIJIIIHDGGIJJIIJHDGEHGIIGCGGGGECEAEHHHFFFDDCECABB?@DCCC?A3 @HWI-1KL150:70:C74KBACXX:1:1101:6748:1978 2:N:0:ATGCCT GTGTGCAGCGGAGCCCTGCACGGGAGACAGGTCTGTCTTCTGCCAGATGGAAGTGCTCGATCGCTACTGCTCCATTCCCGGCTACCACCGGCTCTGCTGTN + CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJDHIIFHJJIIJIJJJJIIJEHHAEEHFFFECCBDDDCCDDDDDDFEEDDDDDDDDDDDDDDDDDCDDDA9 @HWI-1KL150:70:C74KBACXX:1:1101:6964:1994 2:N:0:ATGCCT GGTGGATCTTATATGGGAGGATGCACTGTTCATGTTTGAGTATTTTAAGCCCAAGACCCTTCCTGAATTTGACAGCTATAAGACCAGCACCGTGTCTGCTN + BC@FFFFFHHHGHJJJJIIJHIJJJJJJIJJJJJJJJJJJDHIJJJJJJJGHJJJJJIJIJIJJJJJJJJJIJGHHGHFFFFFFEEEDEDDDDDBBDDDD: @HWI-1KL150:70:C74KBACXX:1:1101:8404:1977 2:N:0:ATGCCT GAAAATAATTCACAAATAGTGTTACAGCTCCATCCACTGAAAATTGTCATAAAAGACATTTTTTCAATGAGTTCATTTTTAGAGAAACCATTCCAGATATC + @CCFFFFFHGHHHJJGHIJCJJIJJJJJJIHGIJJIJJIGIIIIIJIIHHDGGGJJIGIIJJJJGIEHIGJIHIJIJCHEECB@;?BCACECDCDCCCCD- @HWI-1KL150:70:C74KBACXX:1:1101:8836:1977 2:N:0:ATGCCT CACTTTGAAAACTAGAAATCATTACACAAAGTTAAGAACTCACTATTTTAACATGGAGGATGGAGCCTGACATCAGGCCTTTAGGGCACGTTCACCATGCC + CCCFFFFFHHHHHJJIJJJJJJJJJIJJJJJJJIIJJIJJIJIIIJJIJJHGCHIHGIIIJJGHIJJJJJJIJJGGHGHFFFFFDEEDDDDDDDDDDDDDA @HWI-1KL150:70:C74KBACXX:1:1101:9989:1970 2:N:0:ATGCCT AAGAACAAGTTTCTGTACATCTCATTATCATTCTGCCTGTTCACTTGCCTCATGTTTTTGCTGTTCTTCTTTTTGACAGGGATTCGATAAACAAGTGGATN + @@@DDEEDHDHHHEFCEH?FHIIIIHIIIIIGGIIIIIIFFIGGHIECEHBDHGBGCHIIIIIIIIIIIIHGGGE;CCHGHHCFFF@DCA6>CBC@CCCC> @HWI-1KL150:70:C74KBACXX:1:1101:10460:1982 2:N:0:ATGCCT TACATAGGAAGAAAATGCCAATCAAAAATGAAAGTCAGTTAAAACCACTTGAAAGCAATGTCTGTTCCTTTTTAGAATGGAAAGTTGGAGGAAACTTCAGC + CCCFFFFFHHGHHJJJJJJJJJIJJJJJJJJJIJGGGGIJJJJGIDHJJIBFHGHGJGHIEGCHHIIGHHIJIGIGEHHCCHFFFFFC@CDDDCCCCCACC @HWI-1KL150:70:C74KBACXX:1:1101:11860:1969 2:N:0:ATGCCT CCCTGATGGCATAAACACCCCCCCAACAGAGGCAGAGGAGTCGTTTGAATTTGTGGTGGGGGCCCTCACTGGGCAGACGGGGGCCTTCGAGGCTTCAACGN + CCCFFFFFHHHHHJIJJJJJJJJJJIJJJIIJJJJCDG;C.==-=C5.;;.;.(.;.,;'3')5>18(2(4?B2()(+))5>&&)+:4((35&(39(:>&) @HWI-1KL150:70:C74KBACXX:1:1101:12059:1989 2:N:0:ATGCCT GACCCCCCTACCTGTGAGGGGTACAGGACCCTCTGGGGAGGGGCCGCTCCAACAGCTGGCTTCGTTGGTCTGTGCGGGAGGGAGACAGTATTCAGAAGCAA + CCCFFFFFHHHHHJIJIJJJJHIJJJHIIJJJJJJJJJIJIJHFFDDDDDACDDDDDDDDDDDDCDDB?CDDCCCBDD9BBB5<9@?C44@CDDDCCDDDC @HWI-1KL150:70:C74KBACXX:1:1101:12267:1970 2:N:0:ATGCCT AACAGACAAATTTGGAGTTCCTCCAAAGTTCAAACTTTGGAAGACCGTTGAATCAAAAGCCCCAAGCTCAATACCTTTAACATTATTGCCATTGAAGTTCA + CCCFFFFFHHHHHJJIJGIIJJJJJJJJHIJJJJJJJJJJJJJJJIJIIJDGHIIGIIIIJJIIIHHHGHBEFFDFECC@CEECDEDCCCCDCCCCDCD(, @HWI-1KL150:70:C74KBACXX:1:1101:14224:1976 2:N:0:ATGCCT ATGGAAATCAGATGTCCTGTGGTCAAAATCCAGGCTTCCCAGTCAATAAGGATGTCACGCTAACGAGCCCATTGTTGGTCAACTTATTGCAGAGTGACATA + CCCFFFFFHHHDHJJJJJJIHIFIIIJIJJIJJJIJJJIJJJGGGDGIJJGHIIIGGGIIJIJIGIGHHFFFFFFFEDDCCCCDDDDEDDDDAD>@CCCC3 @HWI-1KL150:70:C74KBACXX:1:1101:14302:1968 2:N:0:ATGCCT CACATGCTGCCTGCTTGATCCAGGGTGTGCAGTGGGAACCTGAGGCTTCCGGGAGGGCATGGGGGGGTGATGAGTGCTGCCTGTTCAGGCTCCTCTCCTCT + CCCFFFFFHHHHHIIJIJIIIGIJJFHFHIJJHHJJIJJJIIDHIGJJJJABGFHHHFFFDEDDDDD08<>C>CCCDDCDDCDCDDEDCCBDDCDCC>:?( @HWI-1KL150:70:C74KBACXX:1:1101:14658:1990 2:N:0:ATGCCT AGTAAATTGAAAACCTTCTGAAAAGGTTTCACCATCTTAGACGCCATTAAGAACATTCGTGATTCATGGGAGGAGGTCAAAATATCAACTTTAACAGGAGT + @@?DDDFFHDFFHGHHGIIIGIIIJJCHGHIDHG>GGEIEGIHGIJJJJIFGIIIEGGIJIIGD@FD>DDHEE(;=,>CCEAAACCDCCCA@>:5::<<(, @HWI-1KL150:70:C74KBACXX:1:1101:14850:1985 2:N:0:ATGCCT CACCCTTGAAGTCCCTCCACTCCTGACTGTCCACGATGACGCTGGGGGAGGCAGTGTCCAGGCGTCAGGGCAGTTCTTCCCAGGAGGACCCACAGGAGGCN + CCCFFFFFHHHHHJJJJJJJJIJJJJJJJJJJIJJIJJJJJJJJJJJIHIEHEFFEDDEEEEDDBDDDDDDDDDDDCDDDDDCBDB<BBDD?BBDABBB<& @HWI-1KL150:70:C74KBACXX:1:1101:16090:1965 2:N:0:ATGCCT GCTTCAGCGCACTTCTCCCGACCTACTGGGGCAAACCGAAGGGCGCCCGGGAGCCCGGGCCTTCCGAGGGTGGGCAGTCCCCTGGGGGGGTGGGGGGTGGN + @CCFFFFFHHHHGJGIGIIIFHIGIIGJJJJIHIGBFGAEBGI7=4<A9@>8='8?693&&((+(&&&))8(0&(()((+:+(28@05<9)&&)05&&).9 @HWI-1KL150:70:C74KBACXX:1:1101:16707:1966 2:N:0:ATGCCT GACCATTTACGGTTTCCTCAGTAATTTCCACCAGGATGAATTTCCTTCTCATCACTCTGCCTCAGGTAGTGCTCTGAAGGTCGTCCTTTCTGAACAAACGC + CCCFFFFFHHHHCGIIJJJIJHIIJJJIJJJJJJJJJJJJJJJIJJJJJIDHIIIJJJJJJJIJIJCGIGHIJIJIFHHHFHFFADDDEDDD@CCDDDDD8 @HWI-1KL150:70:C74KBACXX:1:1101:16529:1998 2:N:0:ATGCCT GCCTGGAGATAAGGTAACCCTTAATACTACCTGGAAATAAAAAGAAAATGTCTCTCTCTTTTGGATGCAAGACAGTGACATGGCTTCTCTTTTTCCAGGGN + @BCFFFFFFHHHHJFGHGIJJJJJJIHHJJJJJIIJJJJJJJJJJJJJJJJIIJIJJJJJJJJJJJJJJJIHHHHHFFFFFFFEEEEEDCDDDDDACCDD8 @HWI-1KL150:70:C74KBACXX:1:1101:17676:1982 2:N:0:ATGCCT TCATTTGTTTCTTAGAGGTGTGGTGGCAGCTCAGGTGGCCTAGGATTTGAAATGTGTGTCCCTAACCGGGGTGGTGCTAAGCTTGGGACCAACTGGAGATN + CCCFFFFFHHHHHJJJJJFHIHHFHHGIJJIJGII?FHIHIGIJEEGGGIBGCCBCBBFFIIIJIJJGHFB'9?28::@CDDDDCDBBBDDDDCDCA?9?3 @HWI-1KL150:70:C74KBACXX:1:1101:17886:1973 2:N:0:ATGCCT GAAGCTGGAGGAGAAACTAAAGCCTTATTGAGAAAACATGTTATAGATCCTTTTGTTGCTGAGAGAGGGGAACATAGGTCCTAGACAGGGTGAAGAGTTCT + @@@DDDFF?FD7DDBH;BEHFHEGGIGCHHIGHIIEGH<BGHAAFBF>FB9BDHGGHGIIIEHIIGG(;A9BEF>C@C.>;;>;@CDDDB(5<>>((+:4( @HWI-1KL150:70:C74KBACXX:1:1101:18889:1967 2:N:0:ATGCCT GAGAGGCTCTGATAACATTTATGATCTTAGGATGGAACTTCGTTGTGTCATTGCAATTATTCGTCATGGGGATCGTACTCCCAAGCAGAAGATGAAGATGN + CCCFFFFFHHHHHJIJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJIIGJIBGHJJJJJJJJJJJJJJJCEHGHFEDEFFEEDDABBDDDDDDCDDDDDDD>

[sfchen]

Can you file another issue so that I can track it? And we can close this one now.