I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam and filtered out unpaired reads and reads that didnt align. I then converted the filtered bam to sam and tried to convert the sam to fastq but got the error
Ignoring SAM validation error due to lenient parsing: Error parsing text SAM file. Empty sequence dictionary.; Line 1
at the start of each line and at the end of the file
Exception in thread "main" net.sf.picard.PicardException: Found 1014 unpaired mates at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:158) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175) at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:116)
The same sam file runs OK in cufflinks. I want the fastq files to attempt de novo assembly of the mapped on velvet because the reads were mapped to variant genes with some homology but are predicted to have recombined into novel arrangements.
Thanks for any tips