nohup: ignoring input
GMAP version 2017-10-30 called with args: /gsap/tools/bin/gmap.sse42 -d B73v4_genome_masked -D /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB/ -f gff3_gene -F -t 6 -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 SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 
Finished checking compiler assumptions
Pre-loading compressed genome (oligos)......done (789,876,804 bytes, 192842 pages, 2.63 sec)
Pre-loading compressed genome (bits)......done (789,876,816 bytes, 192842 pages, 2.38 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...Using malloc instead of shmget for file /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB//B73v4_genome_masked/B73v4_genome_masked.ref153offsets64meta
shm_attach not working on file /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB//B73v4_genome_masked/B73v4_genome_masked.ref153offsets64meta, so using memory mapping instead on 134217744 bytes
done (134,217,744 bytes, 0.00 sec)
Allocating memory for ref offsets, kmer 15, interval 3...Using malloc instead of shmget for file /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB//B73v4_genome_masked/B73v4_genome_masked.ref153offsets64strm
shm_attach not working on file /anno/sanyalab/GSAP/GSAP-TESTING/TESTAREA/GMAP-TEST/GMAP-DB//B73v4_genome_masked/B73v4_genome_masked.ref153offsets64strm, so using memory mapping instead on 408708352 bytes
done (408,708,352 bytes, 0.01 sec)
Pre-loading ref positions, kmer 15, interval 3......done (1,082,353,604 bytes, 5.52 sec)
Starting alignment
No paths found for JZ970238.1
No paths found for JZ970218.1
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No paths found for JZ970196.1
No paths found for JZ970199.1
No paths found for JZ970197.1
No paths found for JZ970184.1
No paths found for JZ970182.1

## Lots of output as above ##
## Removed to reduce size  ##

No paths found for FL224557.1
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