Exception in thread "main" java.io.EOFException: Unexpected end of ZLIB input stream
i am trying to do trimming to my data after i do fastqc and determined that my data with bad quality score, but i get error my code is:
1- add my variable files and my adapter
f1="$Home/home/ngs/mouse_project/SRR5017134_Regular_Diet_Tumor_1.fastq.gz"
newf1="$Home/home/ngs/mouse_project/SRR5017134_Regular_Diet_Tumor_1.se.trim.fastq.gz"
adap="$CONDA_PREFIX/share/trimmomatic-0.39-2/adapters"
2-trimming step
trimmomatic SE -threads 1 -phred33 -trimlog trimLogFile -summary statsSummaryFile $f1 $newf1 \
ILLUMINACLIP:$adap/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
i get there in the post title so what is the wrong?
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You probably have corrupt fastq files. Are you able to run FastQC on them without getting an error?
You can use a fastq validation program (https://github.com/nunofonseca/fastq_utils use
fastq_info) to check.Yes, I do I decided to do trimming on my data after running on fastqc