BBmap caused Not in GZIP format

Question

[Ric]

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.

Answer 1

[ATpoint]

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.

[Ric]

Yes, there was plain text and without gz it is working.`