I have a file containing reads. It seems the adapters were removed previously. So I do not need to eliminate the adapters.
When I use fastqc, I have overrepresented sequences in first 7 positions and I want to trim them. That's it.
I wrote this command:
java -jar /usr/local/bin/trimmomatic-0.33.jar SE -phred64 inputfile.fq.gz output.fq.gz HEADCROP:7
Is it wrong?
I get this error:
Exception in thread "main" java.io.IOException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:154)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:75)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:85)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:109)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:105)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:37)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:132)
at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:192)
at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:285)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:40)
How can I do it correctly?
Thanks in advance
When I use fastqc, I have overrepresented sequences in first 7 positions and I want to trim them. That's it.
I wrote this command:
java -jar /usr/local/bin/trimmomatic-0.33.jar SE -phred64 inputfile.fq.gz output.fq.gz HEADCROP:7
Is it wrong?
I get this error:
Exception in thread "main" java.io.IOException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:154)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:75)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:85)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:109)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:105)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:37)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:132)
at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:192)
at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:285)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:40)
How can I do it correctly?
Thanks in advance
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