nohup: ignoring input
GMAP version 2014-06-10 called with args: /mnt/common/rh6/cluster/tdi/bin/gmap -d B73v4_genome_masked -D /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB/ -f gff3_gene -F -t 14 -n 10 -K 50000 --min-identity=0.95 --min-trimmed-coverage=0.90 /anno/sanyalab/PUB_DATASETS/PASA/ZEA/Zea_mays_EST.fasta.clean
Checking compiler assumptions for popcnt: 6B8B4567 clz=1 clz=0 popcount=17 
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Note: >1 sequence detected, so index files are being memory mapped.
  GMAP can run slowly at first while the computer starts to accumulate
  pages from the hard disk into its cache.  To copy index files into RAM
  instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM.
  For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores.
Pre-loading compressed genome (oligos)...,......,.,.,.,...,......,...,.,..,.,.,.,...,...,.,....,.,...,.,.,.,.,.,..,.,..,..,.,..,.,.....,...,.,.,.,.,.,.,..,.,.,..,.,.,.,...,..,.,.,...,....,.,.,...,.,.,.,...,..,..,..,...,..,..,.,.,.,.,.,..,.,..,..,.,.,..,.,..,..,...,..,.,.,..,..,.....,.,.,.,.,.,.,..,.,..,....,.,..,.,.,.,...,.,.,.,.,.,.,.....,...,..,.,.,.,...,.,.,.,.,...,....,...,.,....,.,.,.,.,.,..,.......,...,..,.,.,.,.,.,.,.,.,.,...,..,...,.,.,.....,.,.,..,.,..,.,....,.,..,..,..,.,.,..,...,.,..,.,.,..,....,.,.,....,.,.done (789,876,804 bytes, 192842 pages, 0.67 sec)
Pre-loading compressed genome (bits)...,......,.,.,.,...,......,...,.,..,.,.,.,...,...,.,....,.,...,.,..,.,.,..,.,..,..,.,..,.,.....,...,.,.,.,.,.,.,..,.,.,..,.,.,.,...,..,.,.,...,....,.,.,...,.,.,.,...,..,..,..,...,..,..,.,.,.,.,.,..,.,..,..,.,.,..,.,..,..,...,..,.,.,..,..,.....,.,.,.,.,.,.,..,.,..,....,.,..,.,.,.,...,.,.,.,.,.,.,.....,...,..,.,.,.,...,.,.,.,.,...,....,...,.,....,.,.,.,.,.,..,.......,...,..,.,.,.,.,..,.,.,.,...,..,...,.,.,.....,.,.,..,.,..,.,...,.,.,..,..,..,.,.,..,...,.,..,.,.,..,....,.,.,....,.,.done (789,876,816 bytes, 192842 pages, 0.68 sec)
Looking for index files in directory /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB//B73v4_genome_masked
  Pointers file is B73v4_genome_masked.ref153offsets64meta
  Offsets file is B73v4_genome_masked.ref153offsets64strm
  Positions file is B73v4_genome_masked.ref153positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 15, interval 3...done (134,217,744 bytes, 0.40 sec)
Allocating memory for ref offsets, kmer 15, interval 3...done (408,708,352 bytes, 1.20 sec)
Pre-loading ref positions, kmer 15, interval 3.....................................................................................................................................................................................................................................................................................................................................................................................,.....................................................done (1,082,353,604 bytes, 264247 pages, 0.82 sec)
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## Lots of output as above ##
## Removed to reduce size  ##


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Processed 1756302 queries in 2226.49 seconds (788.82 queries/sec)