We recently ran a set of samples through galaxy from Genewiz. Of our samples, two are not working. Following upload onto Galaxy, we ran these files using HISAT2 version 184.108.40.206 as we did all of our other files. The other files output correctly and were able to be run through htseq and DESeq. However, the output for our problem files following completion of the HISAT is: gzip: input_r.fastq.gz: not in gzip format Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): hisat2-align died with signal 6 (ABRT) (core dumped)
I've tried using the most recent version, re-uploading the files as fastqsanger files, and still receive no output for these files. Genewiz recently sent us their versions of the files which they analyzed and found no problems. Upon uploading these into Galaxy, we encountered the same error. Is there something we can do to resolve this file?