Exception in thread "main" java.lang.RuntimeException: Sequence and quality length don't match

Question

[sansan96]

Hello, I am trying to trimming some data but I have not been able to do it because the process is interrupted, could you help me?

(base) user:~/Enrique_Manuel/aspergillus/trimeados$ java -jar /home/betterlab/Enrique_Manuel/programas/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../DRR178650_1.fastq  ../DRR178650_2.fastq DRR178650_P_1.fastq DRR178650_U_1.fastq DRR178650_P_2.fastq DRR178650_U_2.fastq ILLUMINACLIP:/home/betterlab/Enrique_Manuel/programas/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36

TrimmomaticPE: Started with arguments: ../DRR178650_1.fastq ../DRR178650_2.fastq DRR178650_P_1.fastq DRR178650_U_1.fastq DRR178650_P_2.fastq DRR178650_U_2.fastq ILLUMINACLIP:/home/betterlab/Enrique_Manuel/programas/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Quality encoding detected as phred33

Exception in thread "main" java.lang.RuntimeException: Sequence and quality length don't match: 'TCGGAGTGAACACGAACACTCTGTAGGAGATGACGAAAGCGTGCAGAACAATGACTTTTCGAACGTCCTTCAAGGTATGACTGGTAATGTCGATGTCCAGG' vs 'BBBBBGGGFGGGGGGGFGGGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGEGFEGGGGGGGGGEGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGD*@DRR178650.18192050 18192050 length=101' at org.usadellab.trimmomatic.fastq.FastqRecord.<init>(FastqRecord.java:25) at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:89) at org.usadellab.trimmomatic.fastq.FastqParser.next(FastqParser.java:179) at org.usadellab.trimmomatic.TrimmomaticPE.processSingleThreaded(TrimmomaticPE.java:63) at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:316) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

[sansan96]

The same with fastp:

(base) user:~/Enrique_Manuel/aspergillus/trimeados$ fastp -i ../DRR178650_1.fastq -I ../DRR178650_2.fastq -o DRR178650_P_1.fastq -O DRR178650_P_2.fastq --detect_adapter_for_pe

Detecting adapter sequence for read1...

Illumina TruSeq Adapter Read 1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Detecting adapter sequence for read2...

Illumina TruSeq Adapter Read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

ERROR: sequence and quality have different length: @DRR178650.18192049 18192049 length=101 TCGGAGTGAACACGAACACTCTGTAGGAGATGACGAAAGCGTGCAGAACAATGACTTTTCGAACGTCCTTCAAGGTATGACTGGTAATGTCGATGTCCAGG +DRR178650.18192049 18192049 length=101 BBBBBGGGFGGGGGGGFGGGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGEGFEGGGGGGGGGEGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGD*@DRR178650.18192050 18192050 length=101

Answer 1

[Brian Bushnell]

Your fastq file is corrupt, as you can see from the error message. You need to redownload it and/or try again to make sratoolkit process it correctly. Possibly, posting the commands you are using to create the fastq from the sra might help.

[ATpoint]

Beyond that, do yourself a favor and keep fastq files gzipped. No application ever needs raw text files, they take up space.

[sansan96]

Thanks for the observation and I am actually working with the compressed files but I am getting the same problem, that's why I tried fastq.