holtjma
commented
3 years ago Hello,
Previously when I've seen the "corrupt deflate stream" error, it was caused by a malformed input FASTQ file. For example, you could take a gzipped FASTQ file and cut it at an arbitrary location which would create an invalid gzip file.
I'm not exactly sure what command you're using to generate your FASTQ reads, but it seems to be coming in via a stdin pipe, presumably from whatever program is generating this error at the end:
crisG: Warning - created a read stream for 0 reads.
Exception in thread "main" java.lang.AssertionError
at stream.ConcurrentGenericReadInputStream.(ConcurrentGenericReadInputStream.java:136)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:123)
at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:69)
at jgi.ReformatReads.process(ReformatReads.java:480)
at jgi.ReformatReads.main(ReformatReads.java:52)I suspect that your read generating program is throwing the error for some reason. I suggest running that component separately and storing the file locally somewhere. Then you can check the gzip integrity with gzip -t {filename} to see if there are any issues with the compression format.
Hi, I have encountered this parsing error while running fmlrc2 on Nanopore libraries. Any ideas as to what might be causing it?