Hi,
After removing rRNAs using sortmerna, 2/42 files failed fastqc with error:
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76) at java.lang.Thread.run(Thread.java:745)
I checked the fastq file using fastq_stats which suggested the fastq file is malformed
Malformed fastq record (length mismatch) at line 69042283 Segmentation fault (core dumped)
can anybody please tell me what's the problem in this file?
zcat 4590_END_sortmerna_R2.fastq.gz | sed -n '69042275,69042295p'
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIFIIFIIIIIIFIIIIIFIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFBFFFFFF
@HWI-ST1072:210:C5LGGACXX:4:1309:19821:97176 2:N:0:AGTTCC
CTGGAATCCCTCGATCACTGAACAGGAAGGAAACCTGATGCAGAGACTCAGGACGCAGGCTCCAGAAGTCCCAGACCATGTCCGGATCCTTCAGGTGTGTT
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIBFIIIIFFFIIIIIFFFFFFFFFBBBBBFFBFBFFFFFFBFFFFFFFFBBBBBBBBB
@HWI-ST1072:210:C5LGGACXX:4:1309:19994:97188 2:N:0:AGTTCC
CTCATGTACCGGGGGTTACTGGATGCTCTGCTGCAGACGGCTCGGACAGAGGGCATTTTTGGCATGTACAAGGGAATAGGTGCCTCCTACTTCCGCCTTGG
+
BBBFFFFFFFFFFIIFFIIIIIIIIIIIIIIIIIIIIIFFFFFFFBBBFB<BB7<BFFFFFFBBBBBFFFFFFFBBFBFBBBBFFFFFFFFFFFFFFFFBB
@HWI-ST1072:210:C5LGGACXX:4:1309:19837:97199 2:N:0:AGTTCC
CCTACTTCTCTTTTAATTAAAATGTAGCCACTATATAACAGATATGGTTTACGATCTGTTTCAAAAACATTTACCTAAGTGACTCTGTAAAAACCTCAGCA
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIFIIBFFIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFB
@HWI-ST1072:210:C5LGGACXX:4:1309:19815:97203 2:N:0:AGTTCC
GGGCCATTCGGGGTTGGCTGGGGGTGAGTGGCAGAGCAAGCTTTCAGCACAGGGCGGCATGTGCCAAAAGCACGGTGGCCTGAGGCTGCCCCTCGTGAGCA
+
BBBFFFFFFFFFFFIIIIIIIIFIFFFIFIFIIIIIIFFFFFBFFFFFFF<BBBBBFFFFBBBBFFFFFFBFFFFFFFBFFFFFFF0BBFFFBFFBF<BB0
@HWI-ST1072:210:C5LGGACXX:4:1309:19975:97229 2:N:0:AGTTCC
AGAGACTGCATGGCTTTCATGACGTGAAGATTGGGCACATTCTTGTCTGCCAGCTCCGGGTGCTTGGGCATGTGGACATCCTTCTTGGCCACCATCACCCC
+
Thanks a lot!
I would just like to also report the same problem. I also had corrupted fastq file output after SortMeRNA run and it is also missing lines with quality scores. If someone has sorted out this issue would be grateful if you could share your solution. Thanks