PORT v0.8.3-beta 1/23/2017

• Config file has been updated
  • added HOST_NAME option for head node job submission.

• News
  • added head node job submission option (HOST_NAME in config)
  • intermediate files in gzip format
  • mitochondrial chromosome not filtered (highexp steps deals with highly expressed features).
  • performs intergenic region quantification and outputs spreadsheets (exon-intron-junction level).
  • requests more memory if jobs exit without error (restart_failedjobs_only.pl).
  • sam2genes step splits files into 5million lines in each temp file (2.5million when -norm option is used).
  • delete sam2genes temp files right after cat_genes_files step.
  • delete fasta and blastdb files generated in blast step immediately.
• Bug fixes
  • delete existing temp files before splitting files in sam2genes step.
  • queue update for large datasets (genefilter, run_shuf and make_final_spreadsheet step)
  • request more memory in filtersam step when # of ribosomal reads > 30mil.
  • ribopercents memory 10G -> 3G.
  • but fix in cat_highexp_files.pl
  • sam format check for the entire sam in filtersam step
  • print chromosome list discrepancy warning once.
  • create new STATS directory in PART1 when -alt_out option is used.