Entering edit mode
4.3 years ago
Ric
▴
430
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.
Yes, there was plain text and without gz it is working.`