I'm trying to do an alignment withe a fastq reads from the 1000genomes project. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/sequence_read/ SRR062634.filt.fastq.gz. I'm taking a subset of the SRR file. when I try to run alignment using iPlant via BWA and BWA mem against the reference genome Homo.GRCh38 it gives me a 0 byte output sam file. I've tried this multiple times. my subset file size is around 50kb. original file size is around 25mb. I've checked both original and subset file and both look fine.
You should get an .err or .out file in the output folder that you specified. These files include the console output of bwa and the error message. It is hard to predict what exactly happened without this information.
Fritz's idea is good. But you may also try rerunning the alignment, and make sure the input read files are actually in fastq format. Run through FastQC if you aren't sure from looking at them. I would also recommend trying the Homo.GRCH37 genome. There seem to be some naming issues with the fasta files in the Homom.GRCH38, which can trip up a lot of aligners. Also, if you share your output folder with me through the iPlant Discovery Environment (I'm an iPlant user, too), I may be able to tell you what the problem is.
