Note: gmap.sse42 does not exist. For faster speed, may want to compile package on an SSE4.2 machine
Note: gmap.sse41 does not exist. For faster speed, may want to compile package on an SSE4.1 machine
Note: gmap.ssse3 does not exist. For faster speed, may want to compile package on an SSSE3 machine
GMAP version 2019-06-10 called with args: gmap.sse2 -D ./index/genome_index -d Jure.2_0.gmap -f gff3_gene ./alignments/Jure.2_0.tsa.fa --nthreads=16 --min-intronlength=9 --min-trimmed-coverage=0.95 --min-identity=0.95 -n1
Note: -n 1 will not report chimeric alignments. If you want a single alignment plus chimeras, use -n 0 instead.
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Finished checking compiler assumptions
Pre-loading compressed genome (oligos)......done (215,231,384 bytes, 52547 pages, 0.19 sec)
Pre-loading compressed genome (bits)......done (215,231,424 bytes, 52547 pages, 0.24 sec)
Looking for index files in directory ./index/genome_index/Jure.2_0.gmap
Pointers file is Jure.2_0.gmap.ref153offsets64meta
Offsets file is Jure.2_0.gmap.ref153offsets64strm
Positions file is Jure.2_0.gmap.ref153positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 15, interval 3...Attached new memory for ./index/genome_index/Jure.2_0.gmap/Jure.2_0.gmap.ref153offsets64meta...done (134,217,744 bytes, 0.30 sec)
Allocating memory for ref offsets, kmer 15, interval 3...Attached new memory for ./index/genome_index/Jure.2_0.gmap/Jure.2_0.gmap.ref153offsets64strm...done (328,234,576 bytes, 0.67 sec)
Pre-loading ref positions, kmer 15, interval 3......done (764,009,952 bytes, 0.56 sec)
Starting alignment
No paths found for Jr01_06320_p1
No paths found for Jr01_10100_p1
No paths found for Jr01_13040_p1
No paths found for Jr01_13000_p1
No paths found for Jr01_13020_p1
No paths found for Jr02_01580_p1
No paths found for Jr02_01560_p1
No paths found for Jr02_01690_p1
No paths found for Jr02_01680_p1
No paths found for Jr02_01670_p1
No paths found for Jr02_01660_p1
No paths found for Jr02_01650_p1
No paths found for Jr02_01570_p1
No paths found for Jr02_01590_p1
No paths found for Jr02_01620_p1
No paths found for Jr02_01640_p1
No paths found for Jr02_01710_p1
No paths found for Jr02_01740_p1
No paths found for Jr02_01750_p1
No paths found for Jr02_01730_p1
No paths found for Jr02_01700_p1
No paths found for Jr02_01720_p1
No paths found for Jr02_01610_p1
No paths found for Jr02_01600_p1
No paths found for Jr02_01630_p1
No paths found for Jr02_25650_p1
No paths found for Jr02_23300_p1
No paths found for Jr03_10530_p1
No paths found for Jr03_13080_p1
No paths found for Jr03_15430_p1
No paths found for Jr03_17150_p2
No paths found for Jr03_17150_p1
No paths found for Jr03_20150_p1
No paths found for Jr03_21970_p1
No paths found for Jr03_21960_p1
No paths found for Jr03_22350_p1
No paths found for Jr03_22360_p1
No paths found for Jr03_23530_p1
No paths found for Jr04_01050_p1
No paths found for Jr04_01660_p1
No paths found for Jr04_01690_p1
No paths found for Jr04_01680_p1
No paths found for Jr04_01670_p1
No paths found for Jr04_01700_p1
No paths found for Jr04_01710_p1
No paths found for Jr04_01720_p1
No paths found for Jr04_01730_p1
No paths found for Jr04_21390_p1
No paths found for Jr04_21440_p1
No paths found for Jr05_01120_p1
No paths found for Jr05_02960_p1
No paths found for Jr05_12480_p1
No paths found for Jr05_15370_p1
No paths found for Jr06_04530_p1
No paths found for Jr06_06130_p1
No paths found for Jr06_15860_p1
No paths found for Jr06_19050_p1
No paths found for Jr06_19060_p1
No paths found for Jr07_07810_p1
No paths found for Jr07_17220_p1
No paths found for Jr07_22620_p1
No paths found for Jr08_05220_p1
No paths found for Jr08_05240_p1
No paths found for Jr08_18310_p1
No paths found for Jr08_22120_p1
No paths found for Jr08_22110_p1
No paths found for Jr09_01310_p1
No paths found for Jr09_01320_p1
No paths found for Jr09_13100_p1
No paths found for Jr10_02590_p1
No paths found for Jr10_02600_p1
No paths found for Jr10_15570_p1
No paths found for Jr10_16620_p1
No paths found for Jr10_20550_p1
No paths found for Jr11_03630_p1
No paths found for Jr11_03640_p1
No paths found for Jr11_06780_p1
No paths found for Jr13_03330_p2
No paths found for Jr13_03330_p1
No paths found for Jr13_23950_p1
No paths found for Jr13_25090_p1
No paths found for Jr14_10530_p1
No paths found for Jr15_04400_p1
No paths found for Jr15_06090_p1
No paths found for Jr16_08850_p1
No paths found for Jr16_08870_p1
No paths found for Jr16_20300_p1
Processed 41081 queries in 193.98 seconds (211.78 queries/sec)
Removed existing memory for shmid 32769
Removed existing memory for shmid 0