I was using diffHic and the alignment asks for processing by FixMate and MarkDuplicates from PicardTools, to make the reads mate aware. But, even when using VALIDATION STRINGENCY set to LENIENT or SILENT I hit the same error.
Exception in thread "main" htsjdk.samtools.SAMException: Found two records that are paired, not supplementary, and second of the pair
Any idea How I can solve this issue? Maybe you have encountered it on a rare occasion?
Also on an unrelated note, while using the provided presplit_map.py package for splitted alignments, my exit code returns non-zero because when the script tries to remove the filename provided in allnames using os.remove after pysam.merge it is unable to find the particular file. What is this BAM file? and why is it that during some alignment runs it is found and removed while during others it is never created?
OSError: [Errno 2] No such file or directory: './tmpwPxiCc/SRR1460691_1.0000.bam'