bug (?): non standard FATQ file on paired read #6
Comments
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I am able to reproduce this error, fixing it soon, thanks! |
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The error was caused by that the quality line is started with I have fixed it and released v0.6.1 with this bug fix. Please try again. |
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@Toliman06 could you update this issue once you've tried new fastp release? |
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@sfchen Hi. I installed the new fastp version on my subsamples. The bug is fixed.
Here is the new form of my fastq file: ffcf607a-7b70-4e16-a60b-c09197fa1601_1Mreadshead_windows_W20M30_2.fastq.gz.100lines.fastq
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Can you file another issue so that I can track it? And we can close this one now. |
Dear Developer,
I have some trouble with this application: I'm trying to filter my paired reads fastq files with fastp with two different sets of filters.
Here is a sample of my 2 fastq files (gunzip -c file_X.fastq.gz | tail -n 50):
ffcf607a-7b70-4e16-a60b-c09197fa1601_1.fastq.gz
@HWI-1KL150:70:C74KBACXX:1:1101:1931:1994 1:N:0:ATGCCT NTCTTTCTGACCCTCACTGAGAGCGACCTGAAGGAAATTGGCATCACGTGCGTCCAGAAGGGCCGCTCTGGCCCTCAGCCCGGGGTTGGGGCAAACTCCCA + #1=DFFFFGHFHHIJEIJJIEIJGIIIGIIJFHJICEICGGICIII@GFHIGCHGAHECHFBF=A@?BDDDDDDD8<CCCDD<@BB<>BBBB9?<<ACCD( @HWI-1KL150:70:C74KBACXX:1:1101:3880:1976 1:N:0:ATGCCT NACTTTCTGTTTTTCCTTTATAGCAAGCAACCCAGTGATAGCAGCCCAGCTCTGGTGAGTGTCCTTGAGCTCTAGAGCACAGCTCTCCTCTCTAAGNNNNN + #1=DFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJIIJJJIJJJJJJJJJJIJJJ@GGIDFFGHIIJEIJIJHGHAA>DFFFFECCCCCCDDDEDCCACC3 @HWI-1KL150:70:C74KBACXX:1:1101:4185:1976 1:N:0:ATGCCT NACTCCGGGGCTGCTCTGGACCAGTTTCCATTCCCGTCTCCCCACCCTCACCATCCCTCAGGACATCACGAGTGGTTGCTTGGACCTGAGGTGGACATTCT + #1=DFFFFHHHHHJJJJJJGIJIJFHIGIIIJIJJJGIIIJJJJIJJIJJJHHHHHFFFEECEDEDDDC@?@<BBCDDDCDDBCDDCCCDD>BB<A(4:>( @HWI-1KL150:70:C74KBACXX:1:1101:4438:1971 1:N:0:ATGCCT NCCCAACCAATCAGCCCCAATTTACGATCTATGTAACTCACCAGTTCGATATGCCAATAACCTGGCCTGAACCATGCAGTGCCTTGCAATTTCCTGTGGCA + #1=DDFFFHHHHHJJJJJJJJJJJIJJJJJJJJIJDGIJJJIJJIJIJJIJIIIIIIIGGICHIGHHHGHCFFFE66;@ACCCC@CCCAAC@CDCCCC?B? @HWI-1KL150:70:C74KBACXX:1:1101:4539:1970 1:N:0:ATGCCT NGCAGGCCGCGGACGGAGAGCACGTGAGGGAAGGGGAAGCCGCTCCGGCCTGCGTAGGGGGGGGGGCGGGGCCCCCCGGGACACCCGGGAGGGGGGCGGGN + #4=DDDDDHHDHAGGIDG:;=<FF8C@DDE4?CDEC6>?=;983;?8:&57?85)+0<()5-&&)))0-)&)0&))&&))&&((())&)0&05&0&&&05< @HWI-1KL150:70:C74KBACXX:1:1101:4702:1995 1:N:0:ATGCCT NGGGGTCCTCTGCGGCCAGGGCAGCGCTGCTCAGCATGATGAAGACAAGGATGAGGTTGGTGAAGATGTGGTGGTTGATGAGCTTGTGGGAGCCTACGCGN + #4=DDDFFHHHHHJJJJIHHIJIIJJJJJJJJIIIIJJJJJJJJJJJJHICHHEHFCDFD;?AAC@CCACD(8?',5(4:4>ACC+++(&2?&8((+&&)5 @HWI-1KL150:70:C74KBACXX:1:1101:6121:1971 1:N:0:ATGCCT NGTCCTCCCACCAGCCGGGCACTACTTACATGACGATGAGAGCAGCGTCTCGGGAGTAATCCAGCACAATCTCCTTCAGCCTCACCTGCCGAAGGGCCTGN + #1:BDFFFHHHHGIIIIGFBGIBEH@GECHCHGGGDFHIIIHICEGHGEHIHEH6?5;@3(>(.-(;(55>AC((,,55>?<<C??:9<A9&5)5<(2+(2 @HWI-1KL150:70:C74KBACXX:1:1101:6748:1978 1:N:0:ATGCCT NATCCCGTTGGCTTTCCAGGAGGCTCTGCAGCATCTGCAGGGTCCTGGGGTCCTGGTAAGGGGCTTCCAGGAGTGGAGAAGGGGGGCAGTGAGGTTGGGCC + #1=DFFFDHHHHHJJJJJJJJJJJJIJIJJIFIIIJJJJIJJGIHIIIIJGGIJJJAHIIJHHHFFFEDCE;@?B;5<ABDBBDDB@BB3@ACD?BD>B?( @HWI-1KL150:70:C74KBACXX:1:1101:6964:1994 1:N:0:ATGCCT NGTGGCAATTCTCTTCAGTAGGTTGGCCAAGTCAGCAGACACGGTGCTGGTCTTATAGCTGTCAAATTCAGGAAGGGTCTTGGGCTTAAAATACTCAAACA + #1=DDFFDFHHHHJJJJJHIJJHJJJJJJJJIJJJJJJJJJJJJGHIJJJFGIIIJJJIJIHIJICGGCGGEFHH;B;CC@CDDDDDDCCCEDCDCD:CC5 @HWI-1KL150:70:C74KBACXX:1:1101:8404:1977 1:N:0:ATGCCT NTTTTTCACTCCATTGTTGTTGTTTACCCAGTTTATGGGGGTTGTAATGTTTATCACACTCCTTGGATGATTTCCGAAGGTAAGATATCTGGAATGGTTTT + #4=DDFFFHHHHHGHHFHIFHIGIIIIJJJJBHGIIIIGGI?FGFEHJGGAHIJJJGIGGHHHHHFFFFDCC@CE;3;>@:@>C>ACA@CDCD<AC>ACA< @HWI-1KL150:70:C74KBACXX:1:1101:8836:1977 1:N:0:ATGCCT NGCTGTTTTACAAGTTGGTAGTTTTCTCTTCTTGGCATGGTGAACGTGCCCTAAAGGCCTGATGTCAGGCTCCATCCTCCATGTTAAAATAGTGAGTTCTT + #1=DFDFFHHHHHJJIJJCFHCFIJEHGIJIJJGHEGIIJFEGHDGEIIJHCGIJEGIJGEGHIGIIHIG<AECA7?DDFFFECC(>CC@CC>CCC>C@D: @HWI-1KL150:70:C74KBACXX:1:1101:9989:1970 1:N:0:ATGCCT NTTGTCAACTTTGCTTTTGCTCATGTTGTAATGTTTGGCAATATATGACACATCCACTTGTTTATCGAATCCCTGTCAAAAAGAAGAACAGCAAAAACATN + #1:B=DDDFFFHDGIIIIIGGIEGHBH@9<9FFFHGIIG>FGEGIGDDHG<:9?D@D8?>?FHGGGGGBAG)@;77;4?A;(9?@DFEEA>55=>=;'((, @HWI-1KL150:70:C74KBACXX:1:1101:10460:1982 1:N:0:ATGCCT NCCTATGCAACCTCAGTGTCCACTGAGAAGGGAATCTTGTGGTATGGAACAATGTGGCAAAAAGGTACAAAGTATTCTTACACCTGGAATTCTTAACCTGNffcf607a-7b70-4e16-a60b-c09197fa1601_2.fastq.gz
@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:1:1101:3880:1976 2:N:0:ATGCCT AAAGGGGAAAAAAATTACCAGATGACACACTTCCTGATTTCACTGTAGTAAGGAAAAAGTCAACATTGCAAATAAATACGATCCTTAGAGAGGAGAGCTGT + CCCFFFFFHHHHHJJJJJJJJIJIJJJJJJJJJJJJGIJJJJJJJGHGFHGFIIGJJJJFEHHHGFFFFDF@CCEEEEDDBDBDDCCCDDDDDBBB??CD+ @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 TACATAGGAAGAAAATGCCAATCAAAAATGAAAGTCAGTTAAAACCACTTGAAAGCAATGTCTGTTCCTTTTTAGAATGGAAAGTTGGAGGAAACTTCAGCAs you can see, the file seems to be well formated.
I'm applying 2 different sets of filter:
`fastp -A -L -w 4 -j ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.json -h ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.html -W 20 -M 30 -i ffcf607a-7b70-4e16-a60b-c09197fa1601_1.fastq.gz -I ffcf607a-7b70-4e16-a60b-c09197fa1601_2.fastq.gz -o ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_1.fastq.gz -O fastq_filtered/ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_2.fastq.gz
fastp -A -L -w 4 -j ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.json -h ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.html -q 30 -u 50 -n 5 -i ffcf607a-7b70-4e16-a60b-c09197fa1601_1.fastq.gz -I input_files/ffcf607a-7b70-4e16-a60b-c09197fa1601_2.fastq.gz -o ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_1.fastq.gz -O ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_2.fastq.gz`
here is the log file:
`Read1 before filtering:
total reads: 69722014
total bases: 7041923414
Q20 bases: 6419265369(91.1578%)
Q30 bases: 5704731454(81.011%)
Read1 after filtering:
total reads: 67489520
total bases: 6816441520
Q20 bases: 6312681343(92.6096%)
Q30 bases: 5624025162(82.5068%)
Read2 before filtering:
total reads: 69722014
total bases: 4505725297
Q20 bases: 4505725297(100%)
Q30 bases: 4505725297(100%)
Read2 aftering filtering:
total reads: 67489520
total bases: 4360073359
Q20 bases: 4360073359(100%)
Q30 bases: 4360073359(100%)
Filtering result:
reads passed filter: 134979040
reads failed due to low quality: 4110650
reads failed due to too many N: 354338
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0
JSON report: ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.json
HTML report: ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.html
fastp -A -L -w 4 -j ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.json -h ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_report.html -W 20 -M 30 -i ffcf607a-7b70-4e16-a60b-c09197fa1601_1.fastq.gz -I ffcf607a-7b70-4e16-a60b-c09197fa1601_2.fastq.gz -o ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_1.fastq.gz -O ffcf607a-7b70-4e16-a60b-c09197fa1601_windows_W20M30_2.fastq.gz
fastp v0.6.0, time used: 910 seconds
Read1 before filtering:
total reads: 69722014
total bases: 7041923414
Q20 bases: 6419265369(91.1578%)
Q30 bases: 5704731454(81.011%)
Read1 after filtering:
total reads: 63210865
total bases: 6384297365
Q20 bases: 6031554512(94.4748%)
Q30 bases: 5446376816(85.3089%)
Read2 before filtering:
total reads: 69722014
total bases: 4505725297
Q20 bases: 4505725297(100%)
Q30 bases: 4505725297(100%)
Read2 aftering filtering:
total reads: 63210865
total bases: 4083554985
Q20 bases: 4083554985(100%)
Q30 bases: 4083554985(100%)
Filtering result:
reads passed filter: 126421730
reads failed due to low quality: 12684916
reads failed due to too many N: 337382
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0
JSON report: ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.json
HTML report: ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.html
fastp -A -L -w 4 -j ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.json -h ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_report.html -q 30 -u 50 -n 5 -i ffcf607a-7b70-4e16-a60b-c09197fa1601_1.fastq.gz -I ffcf607a-7b70-4e16-a60b-c09197fa1601_2.fastq.gz -o ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_1.fastq.gz -O ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_2.fastq.gz
fastp v0.6.0, time used: 918 seconds`
the result files look alike:
ffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_1.fastq.gz
@HWI-1KL150:70:C74KBACXX:1:1101:1931:1994 1:N:0:ATGCCT NTCTTTCTGACCCTCACTGAGAGCGACCTGAAGGAAATTGGCATCACGTGCGTCCAGAAGGGCCGCTCTGGCCCTCAGCCCGGGGTTGGGGCAAACTCCCA + #1=DFFFFGHFHHIJEIJJIEIJGIIIGIIJFHJICEICGGICIII@GFHIGCHGAHECHFBF=A@?BDDDDDDD8<CCCDD<@BB<>BBBB9?<<ACCD( @HWI-1KL150:70:C74KBACXX:1:1101:4185:1976 1:N:0:ATGCCT NACTCCGGGGCTGCTCTGGACCAGTTTCCATTCCCGTCTCCCCACCCTCACCATCCCTCAGGACATCACGAGTGGTTGCTTGGACCTGAGGTGGACATTCT + #1=DFFFFHHHHHJJJJJJGIJIJFHIGIIIJIJJJGIIIJJJJIJJIJJJHHHHHFFFEECEDEDDDC@?@<BBCDDDCDDBCDDCCCDD>BB<A(4:>( @HWI-1KL150:70:C74KBACXX:1:1101:4438:1971 1:N:0:ATGCCT NCCCAACCAATCAGCCCCAATTTACGATCTATGTAACTCACCAGTTCGATATGCCAATAACCTGGCCTGAACCATGCAGTGCCTTGCAATTTCCTGTGGCA + #1=DDFFFHHHHHJJJJJJJJJJJIJJJJJJJJIJDGIJJJIJJIJIJJIJIIIIIIIGGICHIGHHHGHCFFFE66;@ACCCC@CCCAAC@CDCCCC?B? @HWI-1KL150:70:C74KBACXX:1:1101:4702:1995 1:N:0:ATGCCT NGGGGTCCTCTGCGGCCAGGGCAGCGCTGCTCAGCATGATGAAGACAAGGATGAGGTTGGTGAAGATGTGGTGGTTGATGAGCTTGTGGGAGCCTACGCGN + #4=DDDFFHHHHHJJJJIHHIJIIJJJJJJJJIIIIJJJJJJJJJJJJHICHHEHFCDFD;?AAC@CCACD(8?',5(4:4>ACC+++(&2?&8((+&&)5 @HWI-1KL150:70:C74KBACXX:1:1101:6121:1971 1:N:0:ATGCCT NGTCCTCCCACCAGCCGGGCACTACTTACATGACGATGAGAGCAGCGTCTCGGGAGTAATCCAGCACAATCTCCTTCAGCCTCACCTGCCGAAGGGCCTGN + #1:BDFFFHHHHGIIIIGFBGIBEH@GECHCHGGGDFHIIIHICEGHGEHIHEH6?5;@3(>(.-(;(55>AC((,,55>?<<C??:9<A9&5)5<(2+(2 @HWI-1KL150:70:C74KBACXX:1:1101:6748:1978 1:N:0:ATGCCT NATCCCGTTGGCTTTCCAGGAGGCTCTGCAGCATCTGCAGGGTCCTGGGGTCCTGGTAAGGGGCTTCCAGGAGTGGAGAAGGGGGGCAGTGAGGTTGGGCC + #1=DFFFDHHHHHJJJJJJJJJJJJIJIJJIFIIIJJJJIJJGIHIIIIJGGIJJJAHIIJHHHFFFEDCE;@?B;5<ABDBBDDB@BB3@ACD?BD>B?( @HWI-1KL150:70:C74KBACXX:1:1101:6964:1994 1:N:0:ATGCCT NGTGGCAATTCTCTTCAGTAGGTTGGCCAAGTCAGCAGACACGGTGCTGGTCTTATAGCTGTCAAATTCAGGAAGGGTCTTGGGCTTAAAATACTCAAACA + #1=DDFFDFHHHHJJJJJHIJJHJJJJJJJJIJJJJJJJJJJJJGHIJJJFGIIIJJJIJIHIJICGGCGGEFHH;B;CC@CDDDDDDCCCEDCDCD:CC5 @HWI-1KL150:70:C74KBACXX:1:1101:8404:1977 1:N:0:ATGCCT NTTTTTCACTCCATTGTTGTTGTTTACCCAGTTTATGGGGGTTGTAATGTTTATCACACTCCTTGGATGATTTCCGAAGGTAAGATATCTGGAATGGTTTT + #4=DDFFFHHHHHGHHFHIFHIGIIIIJJJJBHGIIIIGGI?FGFEHJGGAHIJJJGIGGHHHHHFFFFDCC@CE;3;>@:@>C>ACA@CDCD<AC>ACA< @HWI-1KL150:70:C74KBACXX:1:1101:8836:1977 1:N:0:ATGCCT NGCTGTTTTACAAGTTGGTAGTTTTCTCTTCTTGGCATGGTGAACGTGCCCTAAAGGCCTGATGTCAGGCTCCATCCTCCATGTTAAAATAGTGAGTTCTT + #1=DFDFFHHHHHJJIJJCFHCFIJEHGIJIJJGHEGIIJFEGHDGEIIJHCGIJEGIJGEGHIGIIHIG<AECA7?DDFFFECC(>CC@CC>CCC>C@D: @HWI-1KL150:70:C74KBACXX:1:1101:9989:1970 1:N:0:ATGCCT NTTGTCAACTTTGCTTTTGCTCATGTTGTAATGTTTGGCAATATATGACACATCCACTTGTTTATCGAATCCCTGTCAAAAAGAAGAACAGCAAAAACATN + #1:B=DDDFFFHDGIIIIIGGIEGHBH@9<9FFFHGIIG>FGEGIGDDHG<:9?D@D8?>?FHGGGGGBAG)@;77;4?A;(9?@DFEEA>55=>=;'((, @HWI-1KL150:70:C74KBACXX:1:1101:10460:1982 1:N:0:ATGCCT NCCTATGCAACCTCAGTGTCCACTGAGAAGGGAATCTTGTGGTATGGAACAATGTGGCAAAAAGGTACAAAGTATTCTTACACCTGGAATTCTTAACCTGN + #4BDFFFFHHHHHJJJIJJJJJJJJGJIJJJIFHGIJJJHIIFHIGIGJJGIIIIGGJJJJJGGG)=;CDHE=AC7ADEFFFFDDEE<CCA@DED;C@@BD @HWI-1KL150:70:C74KBACXX:1:1101:11860:1969 1:N:0:ATGCCT NACCTTGTCCTTGGCACTGCGGCAGCCTTGCAGGCTGGCAAGGATCTGGGCCTGCACACTCTGAACCCACAGCTCCCGCTCCTCCGCCGTTGAAGCCTCNN + #1=DDFFFHHHHHJJIJJJJJJJIJIJIJJIJJJIJJJEFHGI=CFGEGF2CCACEHHGBFDECAABB?@?ABC>58?BDDBACABBD>99?2@A:<A<0) @HWI-1KL150:70:C74KBACXX:1:1101:12222:1966 1:N:0:ATGCCT NAGCTTAAACAGTGGGTTTTTCAATGTCTCTCTTTAGGATTTTTGCTGGGTAAAAGCCTGTTTTACGCGTGGAATGCACACCTCCGGCCAACGGAGACTCCffcf607a-7b70-4e16-a60b-c09197fa1601_bases_q30u50n5_2.fastq.gz
@HWI-1KL150:70:C74KBACXX:1:1101:1931:1994 2:N:0:ATGCCT ACAGCCTGCGGGGGGAATGTGACCAGGATATGCCTCAGCGTCCCAAGAGCGCTTACATGAGTGGGAGTTTGCCCCAACCCCGGGCTGAGGGCCAGAGCGGC + KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK + CCCFFFFFHHHHHJJJJJJJJIJIJJJJJJJJJJJJGIJJJJJJJGHGFHGFIIGJJJJFEHHHGFFFFDF@CCEEEEDDBDBDDCCCDDDDDBBB??CD+ @HWI-1KL150:70:C74KBACXX:1:1101:4185:1976 2:N:0:ATGCCT KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK ACACTAGCCACTCACGTTCCATCTCTTCCTCGGAGAAATCCTCAGGCCCAGCCAAGGGCAGGAGCAAAAAGGGGAGAATGTCCACCTCAGGTCCAAGCAAC + CCCFFFFFHHHHHJJJHIIJJJIJJJJJJIJJIJJJJJJIJJJJJJIIJJFHIJIJJJIIHHGFFFFDDDDDDD@BBDDDDDDDDDDDDDD@CDD>CBBDA K CCCFFFFFHHHHHJJJHIJJJJJJJIJJJIJJIJIJJJJJIIIIJJIJIIDDEIGGHJHGGGIIIGGDGHIJJJHHHHFFFCDECCCEECDCCDCCCD??3 @HWI-1KL150:70:C74KBACXX:1:1101:4539:1970 2:N:0:ATGCCT GGCCTCGTGCGCTCGGGCCCGCACGCCGTTGTTCGCGTCACCCCCACCCAGCTCCCTTCCGCGTGTGCTCGGAGGGCGCGGCGCACCGCCTACGCAGGCCN KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK + CCCFFFFFHHHHHJJJJIJJJJJJJJJJIJHEHHFFDDBDDDDDDDDDDDDDDDDDDDDDDDDBDBDDDCDD;BBDDDDDDBD@BDDDD<<>CDDBBDDD> @HWI-1KL150:70:C74KBACXX:1:1101:4702:1995 2:N:0:ATGCCT KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK CAAGCAGCGGCTTTTCCCTGCAGGATCCGCGTAGGCTGCCACAAGCTCATCAACCACCACATCTTCACCAACCTCATCCTTGTCTTCATCATGCTGAGCAN + CCCFFFFFHHHHHJJJIIIIJIJJJIJJIJJEHEIIIIDGHIGIAEHHHH?@DEFFDDDDDCDCDEDDD>B@BCDCCDDACDCDDDDEEE@CDDCCCBDD3 K @HWI-1KL150:70:C74KBACXX:1:1101:6121:1971 2:N:0:ATGCCT AGACAGGAGACTCTATAAGAATTTATGAGGCAGCAGAGTCTACAAGTAAATCATGAATCCAGTTGAAAATGTTAATGAGGCCATAGACGTGGTGAAGGATT + KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK @C@DFFFFHHHGHJJJJIIIHIIJJJJIGIJJJJIIIJGHIJIIIJIIIHDGGIJJIIJHDGEHGIIGCGGGGECEAEHHHFFFDDCECABB?@DCCC?A3 @HWI-1KL150:70:C74KBACXX:1:1101:6748:1978 2:N:0:ATGCCT GTGTGCAGCGGAGCCCTGCACGGGAGACAGGTCTGTCTTCTGCCAGATGGAAGTGCTCGATCGCTACTGCTCCATTCCCGGCTACCACCGGCTCTGCTGTN KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK + CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJDHIIFHJJIIJIJJJJIIJEHHAEEHFFFECCBDDDCCDDDDDDFEEDDDDDDDDDDDDDDDDDCDDDA9 @HWI-1KL150:70:C74KBACXX:1:1101:6964:1994 2:N:0:ATGCCT KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK GGTGGATCTTATATGGGAGGATGCACTGTTCATGTTTGAGTATTTTAAGCCCAAGACCCTTCCTGAATTTGACAGCTATAAGACCAGCACCGTGTCTGCTN + BC@FFFFFHHHGHJJJJIIJHIJJJJJJIJJJJJJJJJJJDHIJJJJJJJGHJJJJJIJIJIJJJJJJJJJIJGHHGHFFFFFFEEEDEDDDDDBBDDDD: K @HWI-1KL150:70:C74KBACXX:1:1101:8404:1977 2:N:0:ATGCCT GAAAATAATTCACAAATAGTGTTACAGCTCCATCCACTGAAAATTGTCATAAAAGACATTTTTTCAATGAGTTCATTTTTAGAGAAACCATTCCAGATATC + KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK @CCFFFFFHGHHHJJGHIJCJJIJJJJJJIHGIJJIJJIGIIIIIJIIHHDGGGJJIGIIJJJJGIEHIGJIHIJIJCHEECB@;?BCACECDCDCCCCD- @HWI-1KL150:70:C74KBACXX:1:1101:8836:1977 2:N:0:ATGCCT CACTTTGAAAACTAGAAATCATTACACAAAGTTAAGAACTCACTATTTTAACATGGAGGATGGAGCCTGACATCAGGCCTTTAGGGCACGTTCACCATGCC KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK + CCCFFFFFHHHHHJJIJJJJJJJJJIJJJJJJJIIJJIJJIJIIIJJIJJHGCHIHGIIIJJGHIJJJJJJIJJGGHGHFFFFFDEEDDDDDDDDDDDDDAThe other files look alike (file_1 is normal, file_2 has some extra "KKKKKK" lines...)
When trying to align data on genome with BWA MEM, only 3 sequences seems to be well formated in my file.
This is probably due to the non canonical format of my fastq reads with the extra lines.
Do you have any idea why this doesn't work?
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