Yes, there was plain text and without gz it is working.`
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Hi, is there a way to support gz files in partition.sh?
java -ea -Xmx1g -cp /miniconda2/envs/bbmap/opt/bbmap-38.73-0/current/ jgi.PartitionReads in=faspt-rm_adapters_correction_R1.fq.gz in2=faspt-rm_adapters_correction_R2.fq.gz out=split-fastq/faspt-rm_adapters_correction_R1.%.fq.gz out2=split-fastq/faspt-rm_adapters_correction_R2.%.fq.gz ways=1000
Executing jgi.PartitionReads [in=faspt-rm_adapters_correction_R1.fq.gz, in2=faspt-rm_adapters_correction_R2.fq.gz, out=split-fastq/faspt-rm_adapters_correction_R1.%.fq.gz, out2=split-fastq/faspt-rm_adapters_correction_R2.%.fq.gz, ways=1000]
Set INTERLEAVED to false
Error when attempting to read faspt-rm_adapters_correction_R1.fq.gz
Exception in thread "main" java.lang.RuntimeException: java.util.zip.ZipException: Not in GZIP format
at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1048)
at fileIO.ReadWrite.getInputStream(ReadWrite.java:848)
at fileIO.ByteFile1.open(ByteFile1.java:330)
at fileIO.ByteFile1.<init>(ByteFile1.java:100)
at fileIO.ByteFile.makeByteFile(ByteFile.java:38)
at fileIO.ByteFile.makeByteFile(ByteFile.java:27)
at stream.FastqReadInputStream.<init>(FastqReadInputStream.java:59)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:111)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:64)
at jgi.PartitionReads.process(PartitionReads.java:241)
at jgi.PartitionReads.main(PartitionReads.java:42)
Caused by: java.util.zip.ZipException: Not in GZIP format
at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:166)
at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:80)
at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1042)
... 10 more
Thank you in advance.
bbmap supports gzipped files. Your file is apparently not gzipped. What is the output of file faspt-rm_adapters_correction_R1.fq.gz? Also try head faspt-rm_adapters_correction_R1.fq.gz? Maybe it carries the gz extension but is plain text. In that case output of head will be human readable text.
Yes, there was plain text and without gz it is working.`
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