[seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/smallerInsert/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq -2 /gscratch/srlab/data/CanuTest/smallerInsert/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq -S 151114_aligned.sam 61248273 reads; of these: 61248273 (100.00%) were paired; of these: 48302155 (78.86%) aligned concordantly 0 times 4356027 (7.11%) aligned concordantly exactly 1 time 8590091 (14.03%) aligned concordantly >1 times ---- 48302155 pairs aligned concordantly 0 times; of these: 541472 (1.12%) aligned discordantly 1 time ---- 47760683 pairs aligned 0 times concordantly or discordantly; of these: 95521366 mates make up the pairs; of these: 80084381 (83.84%) aligned 0 times 3215848 (3.37%) aligned exactly 1 time 12221137 (12.79%) aligned >1 times 34.62% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/smallerInsert/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq -2 /gscratch/srlab/data/CanuTest/smallerInsert/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq -S 151114-66_aligned.sam 58749332 reads; of these: 58749332 (100.00%) were paired; of these: 56836795 (96.74%) aligned concordantly 0 times 211727 (0.36%) aligned concordantly exactly 1 time 1700810 (2.90%) aligned concordantly >1 times ---- 56836795 pairs aligned concordantly 0 times; of these: 2441437 (4.30%) aligned discordantly 1 time ---- 54395358 pairs aligned 0 times concordantly or discordantly; of these: 108790716 mates make up the pairs; of these: 78394432 (72.06%) aligned 0 times 4889980 (4.49%) aligned exactly 1 time 25506304 (23.45%) aligned >1 times 33.28% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/smallerInsert/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq -2 /gscratch/srlab/data/CanuTest/smallerInsert/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq -S 151118-96_aligned.sam 40482782 reads; of these: 40482782 (100.00%) were paired; of these: 28962127 (71.54%) aligned concordantly 0 times 3197188 (7.90%) aligned concordantly exactly 1 time 8323467 (20.56%) aligned concordantly >1 times ---- 28962127 pairs aligned concordantly 0 times; of these: 73008 (0.25%) aligned discordantly 1 time ---- 28889119 pairs aligned 0 times concordantly or discordantly; of these: 57778238 mates make up the pairs; of these: 51701740 (89.48%) aligned 0 times 1538809 (2.66%) aligned exactly 1 time 4537689 (7.85%) aligned >1 times 36.14% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq -S 160103_62.sam 76114318 reads; of these: 76114318 (100.00%) were paired; of these: 74523544 (97.91%) aligned concordantly 0 times 257235 (0.34%) aligned concordantly exactly 1 time 1333539 (1.75%) aligned concordantly >1 times ---- 74523544 pairs aligned concordantly 0 times; of these: 1098101 (1.47%) aligned discordantly 1 time ---- 73425443 pairs aligned 0 times concordantly or discordantly; of these: 146850886 mates make up the pairs; of these: 102722206 (69.95%) aligned 0 times 9357854 (6.37%) aligned exactly 1 time 34770826 (23.68%) aligned >1 times 32.52% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq -S 160103_75.sam 33193824 reads; of these: 33193824 (100.00%) were paired; of these: 32693208 (98.49%) aligned concordantly 0 times 121478 (0.37%) aligned concordantly exactly 1 time 379138 (1.14%) aligned concordantly >1 times ---- 32693208 pairs aligned concordantly 0 times; of these: 313109 (0.96%) aligned discordantly 1 time ---- 32380099 pairs aligned 0 times concordantly or discordantly; of these: 64760198 mates make up the pairs; of these: 44768890 (69.13%) aligned 0 times 4447142 (6.87%) aligned exactly 1 time 15544166 (24.00%) aligned >1 times 32.56% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq -S 160103_I137_FCH3V5YBBXX_L4-62.sam 74772608 reads; of these: 74772608 (100.00%) were paired; of these: 73189329 (97.88%) aligned concordantly 0 times 256537 (0.34%) aligned concordantly exactly 1 time 1326742 (1.77%) aligned concordantly >1 times ---- 73189329 pairs aligned concordantly 0 times; of these: 1072696 (1.47%) aligned discordantly 1 time ---- 72116633 pairs aligned 0 times concordantly or discordantly; of these: 144233266 mates make up the pairs; of these: 100891188 (69.95%) aligned 0 times 9181648 (6.37%) aligned exactly 1 time 34160430 (23.68%) aligned >1 times 32.53% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq -S 160103_I137_FCH3V5YBBXX_L4_75.sam 31504848 reads; of these: 31504848 (100.00%) were paired; of these: 31015335 (98.45%) aligned concordantly 0 times 118302 (0.38%) aligned concordantly exactly 1 time 371211 (1.18%) aligned concordantly >1 times ---- 31015335 pairs aligned concordantly 0 times; of these: 296016 (0.95%) aligned discordantly 1 time ---- 30719319 pairs aligned 0 times concordantly or discordantly; of these: 61438638 mates make up the pairs; of these: 42420168 (69.04%) aligned 0 times 4211381 (6.85%) aligned exactly 1 time 14807089 (24.10%) aligned >1 times 32.68% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq -S 160103_I137_FCH3V5YBBXX_L5_74.sam 81999890 reads; of these: 81999890 (100.00%) were paired; of these: 80126239 (97.72%) aligned concordantly 0 times 271971 (0.33%) aligned concordantly exactly 1 time 1601680 (1.95%) aligned concordantly >1 times ---- 80126239 pairs aligned concordantly 0 times; of these: 1506806 (1.88%) aligned discordantly 1 time ---- 78619433 pairs aligned 0 times concordantly or discordantly; of these: 157238866 mates make up the pairs; of these: 111647450 (71.00%) aligned 0 times 9182951 (5.84%) aligned exactly 1 time 36408465 (23.15%) aligned >1 times 31.92% overall alignment rate [seanb80@n2193 alignments]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 -p 26 -x oly_pacbio.contigs.bt2 -1 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq -2 /gscratch/srlab/data/CanuTest/largerInsert/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq -S 160103_I137_FCH3V5YBBXX_L6_74.sam 80404249 reads; of these: 80404249 (100.00%) were paired; of these: 78568206 (97.72%) aligned concordantly 0 times 265284 (0.33%) aligned concordantly exactly 1 time 1570759 (1.95%) aligned concordantly >1 times ---- 78568206 pairs aligned concordantly 0 times; of these: 1472647 (1.87%) aligned discordantly 1 time ---- 77095559 pairs aligned 0 times concordantly or discordantly; of these: 154191118 mates make up the pairs; of these: 109570559 (71.06%) aligned 0 times 8979905 (5.82%) aligned exactly 1 time 35640654 (23.11%) aligned >1 times 31.86% overall alignment rate