Error in trimmomatic

Question

[Anderson Stiward]

Hi! Trust you are well. I am trying to run this program but I get the following error and I dont know to fix it neither understand it. Could you help me please?

java -jar trimmomatic-0.36.jar PE -phred33 white_replicate1.R1paired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R1paired.fq.gz white_replicate1.R1unpaired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R2unpaired.fq.gz ILLUMINACLIP:/mnt/g/poolseq_tutorial_1/poolseq_tutorial/adapters/TruSeq3-

PE.fa:2:20:10:1:true TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:30 TOPHRED33

TrimmomaticPE: Started with arguments:
 -phred33 white_replicate1.R1paired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R1paired.fq.gz white_replicate1.R1unpaired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R2unpaired.fq.gz ILLUMINACLIP:/mnt/g/poolseq_tutorial_1/poolseq_tutorial/adapters/TruSeq3-PE.fa:2:20:10:1:true TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:30 TOPHRED33
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 "main" java.io.EOFException: Unexpected end of ZLIB input stream
        at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
        at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
        at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:116)
        at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.read(ConcatGZIPInputStream.java:73)
        at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:283)
        at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:325)
        at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:177)
        at java.io.InputStreamReader.read(InputStreamReader.java:184)
        at java.io.BufferedReader.fill(BufferedReader.java:154)
        at java.io.BufferedReader.readLine(BufferedReader.java:317)
        at java.io.BufferedReader.readLine(BufferedReader.java:382)
        at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:71)
        at org.usadellab.trimmomatic.fastq.FastqParser.next(FastqParser.java:179)
        at org.usadellab.trimmomatic.TrimmomaticPE.processSingleThreaded(TrimmomaticPE.java:62)
        at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:311)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:539)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

THANK YOU!

Answer 1

[Pierre Lindenbaum]

Unexpected end of ZLIB input stream

there is a problem with your fastq files. Test with

gunzip -t  white_replicate1.R1paired.fq.gz white_replicate1.R2paired.fq.gz

[Anderson Stiward]

Thank you so much Mr. Pierre!