nohup: ignoring input
GMAP version 2017-11-15 called with args: /anno/sanyalab/SOFTWARE/gmap-2017-11-15/bin/gmap.sse42 -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_cDNA.fasta
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, 0.68 sec)
Pre-loading compressed genome (bits)......done (789,876,816 bytes, 192842 pages, 2.13 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, 0.00 sec)
Pre-loading ref positions, kmer 15, interval 3......done (1,082,353,604 bytes, 0.88 sec)
Starting alignment
No paths found for AY107948.1
No paths found for AH005059.2
No paths found for AF439733.1
No paths found for AY109468.1
No paths found for AY109785.1
No paths found for AY109498.1
No paths found for AF439724.1
No paths found for AY109356.1
No paths found for AF439726.1
No paths found for AY110418.1
No paths found for AF261942.1
No paths found for AF099441.1
No paths found for AF099433.1
No paths found for AY104405.1
No paths found for AF439728.1
No paths found for AF439722.1
No paths found for AF099376.1


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


No paths found for XM_020548210.1
No paths found for XM_020548182.1
No paths found for XM_020548183.1
No paths found for XM_020548029.1
No paths found for XM_020549813.1
No paths found for XM_020549815.1
No paths found for XM_020548772.1
No paths found for XM_020548746.1
No paths found for XM_020548728.1
No paths found for Z21721.1
No paths found for Y12762.1
No paths found for Y09636.1
No paths found for Z29512.1
No paths found for XM_020548309.1
Processed 229921 queries in 1153.64 seconds (199.30 queries/sec)