Trimmomatic: Missing sequence line from record

Question

[ddzhangzz]

My RNASeq data appear about 3% adapter contamination and I was trying to trim them using Trimmomatic (v.0.36) but it seems it doesn't work correctly. I got below message a second after I run the program: TrimmomaticPE: Started with arguments:

-threads 8 -phred33 -trimlog DRR091550log DRR091550_1.fastq.bz2 DRR091550_2.fastq.bz2 DRR091550_forward_paired.fastq.bz2 DRR091550_forward_unpaired.fastq.bz2 DRR091550_reverse_paired.fastq.bz2 DRR091550_reverse_unpaired.fastq.bz2 ILLUMINACLIP:TruSeq3PE.fa:1:30:10 
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences

Exception in thread "Thread-0" Exception in thread "Thread-1" java.lang.RuntimeException: Missing sequence line from record: DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 length
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Input Read Pairs: 2000 Both Surviving: 1953 (97.65%) Forward Only Surviving: 47 (2.35%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)                                                                                                                                                                       
TrimmomaticPE: Completed successfully

Then I checked the record DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 and it seems nothing wrong:

@DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 length=101
GGGAGAGAAGAAGGGCATGGCCAGAAGGCAAGCCCCGCAGAAGGCAGCTTAACGGTACTTGGAGGTCAGCACGGTGCTCACAGAGGCAAGGAATTTGTCCA
+DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 length=101
CCCDFFFFGFHHHJJJJJIEIJJJJJJJJJJJIJJJJJJJJIIJIJGJHHGHHFFEDDEFCECDB=ACDDDDDD?<@CDDDDDDDDBDDDDDDCDDDCCD>

@DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 length=101
CCGATTTCACCCCCGCGGTGCATGCCTCTCTGGACAAATTCCTTGCCTCTGTGAGCACCGTGCTGACCTCCAAGTACCGTTAAGCTGCCTTCTGCGGGGCT
+DRR091550.2646 HWI-ST886:245:C1T77ACXX:7:1101:17633:2535 length=101
CCCFFFFFHHHHHJJJJJJJJIJIIJJJJJJIJIJJJJJJHGIJIJJIJGHEHHHFFFFDDDDDDDDDDDDDCDDDDDDDBBDDDDDDDDDDDDDD@BDDD

Does somebody have some suggestions?

[wdemos]

Was there any resolution for this question? I am running into the same error

[GenoMax]

Validate that your fastq files are not corrupt. You can use fq lint: https://github.com/stjude-rust-labs/fq