Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.2])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/modules/uri_apps/software/SAMtools/1.14-GCC-11.2.0/bin/samtools'
Reference genome folder provided is ../data/ (absolute path is '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/)'
FastQ format assumed (by default)
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4
Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary!
Input files to be analysed (in current folder '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code'):
../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R1_001.fastq.gz
../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R2_001.fastq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/
Setting parallelization to single-threaded (default)
Summary of all aligner options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code
Now reading in and storing sequence information of the genome specified in: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/
Single-core mode: setting pid to 1
Paired-end alignments will be performed
=======================================
The provided filenames for paired-end alignments are ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R2_001.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file trimmed_ACR-140-TP2_S5_R1_001.fastq.gz to trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_ACR-140-TP2_S5_R1_001.fastq.gz to trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_G_to_A.fastq
Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-140-TP2_S5_R1_001.fastq.gz (253975571 sequences in total)
Writing a C -> T converted version of the input file trimmed_ACR-140-TP2_S5_R2_001.fastq.gz to trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_ACR-140-TP2_S5_R2_001.fastq.gz to trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_G_to_A.fastq
Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-140-TP2_S5_R2_001.fastq.gz (253975571 sequences in total)
Input files are trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:1866:1014_1:N:0:AATGCCTC+TNGATCGA/1 77 * 0 0 * * 0 0 TNTTTTATATTAGTATAGGAAAATAATTAAAATTGGTAAATGATGTGATGTTATTAATATTTTTTTTGATTTGGATAAGGGAGATTTTTTATTTGGGTTTAGGATGTTGTTT I#IIII9IIII9II9I9IIIIII9I9II9-9-IIIII9I9II9IIIII9IIIIIIIIIIIII9IIIII9IIIII9-I9I9III-II-I9I-III9IIII9IIIIIIIIIIII YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:1866:1014_2:N:0:AATGCCTC+TNGATCGA/2 141 * 0 0 * * 0 0 AAACAACATCCTAAACCCAAATAAAAAATCTCCCTTATCCAAATCAAAAAAAATATTAATAACATCACATCATTTACCAATTTTAATTATTTTCCTATACTAATATAAAAAA IIIIIII9III9IIIII9IIIIIIIII99III9-I9I9I9IIIIII9-99-99-I-I-9III9IIII--II-II-II9III9IIII9I9-I9-99I-I9999IIIIII---9 YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:1866:1014_1:N:0:AATGCCTC+TNGATCGA/1 77 * 0 0 * * 0 0 TNTTTTATATTAATATAAAAAAATAATTAAAATTAATAAATAATATAATATTATTAATATTTTTTTTAATTTAAATAAAAAAAATTTTTTATTTAAATTTAAAATATTATTT I#IIII9IIII9II9I9IIIIII9I9II9-9-IIIII9I9II9IIIII9IIIIIIIIIIIII9IIIII9IIIII9-I9I9III-II-I9I-III9IIII9IIIIIIIIIIII YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:1866:1014_2:N:0:AATGCCTC+TNGATCGA/2 141 * 0 0 * * 0 0 AAATAATATTTTAAATTTAAATAAAAAATTTTTTTTATTTAAATTAAAAAAAATATTAATAATATTATATTATTTATTAATTTTAATTATTTTTTTATATTAATATAAAAAA IIIIIII9III9IIIII9IIIIIIIII99III9-I9I9I9IIIIII9-99-99-I-I-9III9IIII--II-II-II9III9IIII9I9-I9-99I-I9999IIIIII---9 YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:1866:1014_1:N:0:AATGCCTC+TNGATCGA/1 77 * 0 0 * * 0 0 TNTTTTATATTAATATAAAAAAATAATTAAAATTAATAAATAATATAATATTATTAATATTTTTTTTAATTTAAATAAAAAAAATTTTTTATTTAAATTTAAAATATTATTT I#IIII9IIII9II9I9IIIIII9I9II9-9-IIIII9I9II9IIIII9IIIIIIIIIIIII9IIIII9IIIII9-I9I9III-II-I9I-III9IIII9IIIIIIIIIIII YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:1866:1014_2:N:0:AATGCCTC+TNGATCGA/2 141 * 0 0 * * 0 0 AAATAATATTTTAAATTTAAATAAAAAATTTTTTTTATTTAAATTAAAAAAAATATTAATAATATTATATTATTTATTAATTTTAATTATTTTTTTATATTAATATAAAAAA IIIIIII9III9IIIII9IIIIIIIII99III9-I9I9I9IIIIII9-99-99-I-I-9III9IIII--II-II-II9III9IIII9I9-I9-99I-I9999IIIIII---9 YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:1866:1014_1:N:0:AATGCCTC+TNGATCGA/1 83 ptg000002l_GA_converted 14467024 42 112M = 14467024 -112 AAACAACATCCTAAACCCAAATAAAAAATCTCCCTTATCCAAATCAAAAAAAATATTAATAACATCACATCATTTACCAATTTTAATTATTTTCCTATACTAATATAAAANA IIIIIIIIIIII9IIII9III-I9I-II-III9I9I-9IIIII9IIIII9IIIIIIIIIIIII9IIIII9II9I9IIIII-9-9II9I9IIIIII9I9II9IIII9IIII#I AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:29T80A1 YS:i:-6 YT:Z:CP
LH00260:131:22L7V3LT4:3:1101:1866:1014_2:N:0:AATGCCTC+TNGATCGA/2 163 ptg000002l_GA_converted 14467024 42 112M = 14467024 112 AAACAACATCCTAAACCCAAATAAAAAATCTCCCTTATCCAAATCAAAAAAAATATTAATAACATCACATCATTTACCAATTTTAATTATTTTCCTATACTAATATAAAAAA IIIIIII9III9IIIII9IIIIIIIII99III9-I9I9I9IIIIII9-99-99-I-I-9III9IIII--II-II-II9III9IIII9I9-I9-99I-I9999IIIIII---9 AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:29T82 YS:i:-7 YT:Z:CP
>>> Writing bisulfite mapping results to trimmed_ACR-140-TP2_S5_pe.bam <<<
Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R2_001.fastq.gz
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:40684:6015_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625676
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1104:12361:22712_1:N:0:AATGTCTC+TGGATCGA ptg000002l 1
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1110:49189:7710_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625628
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1113:27017:2499_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625653
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1117:34421:14195_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1122:8574:1168_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1123:40231:28511_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625582
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1124:25107:10791_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1124:51496:25738_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625577
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1129:47449:10861_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625577
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1129:47466:10861_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625577
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1139:38928:15610_1:N:0:AATGCCTC+TGGATCGA ptg000095l 40245
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1141:13745:14153_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625612
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1141:13737:14167_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625612
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1141:13753:14167_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625612
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1149:2958:8228_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625571
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1158:46940:12977_1:N:0:AATGTCTC+TGGATCGA ptg000025l 1
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1163:4569:27909_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625630
Processed 20000000 sequence pairs so far
Processed 21000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1167:31184:28875_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625576
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1170:38588:4964_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625593
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1173:25188:21633_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625603
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1174:36501:8298_1:N:0:AATGCCTC+TGGATCGA ptg000002l 1
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:23812:4712_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625630
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:33393:28553_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1178:23270:25009_1:N:0:AATGCCTC+TGGATCGA ptg000140l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1178:23262:25023_1:N:0:AATGCCTC+TGGATCGA ptg000140l 2
Processed 25000000 sequence pairs so far
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Processed 28000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1188:19887:16857_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1188:19895:16871_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1192:13939:27068_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1193:37625:21563_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 31000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1197:15890:23328_1:N:0:AATGCCTC+TGGATCGA ptg000036l 6407221
Processed 32000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1202:39292:14644_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625573
Processed 33000000 sequence pairs so far
Processed 34000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1207:39292:10245_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625617
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1208:3363:22264_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625639
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1210:25034:10301_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625636
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1213:2618:18538_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625625
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1214:29088:26480_1:N:0:AATGCCTC+TGGATCGA ptg000090l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1214:24387:28651_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625593
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1215:27761:21605_1:N:0:AATGCCTC+TGGATCGA ptg000038l 3
Processed 37000000 sequence pairs so far
Processed 38000000 sequence pairs so far
Processed 39000000 sequence pairs so far
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1227:26199:16268_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625572
Processed 41000000 sequence pairs so far
Processed 42000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1234:6834:14405_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625617
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1235:29736:25023_1:N:0:AATGCCTC+TGGATCGA ptg000007l 12295913
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1236:36169:18538_1:N:0:AATGCCTC+TGGATCGA ptg000135l 25289
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1240:41866:12094_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625571
Processed 45000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1242:18536:23370_1:N:0:AATGTCTC+TGGATCGA ptg000109l 39607
Processed 46000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1246:46559:21563_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625583
Processed 47000000 sequence pairs so far
Processed 48000000 sequence pairs so far
Processed 49000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1255:7725:9447_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625573
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1256:8485:20625_1:N:0:AATGCCTC+TGGATCGA ptg000002l 1
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1258:32616:11548_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625655
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1258:35068:18538_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625654
Processed 51000000 sequence pairs so far
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1268:21392:1280_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625578
Processed 54000000 sequence pairs so far
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Processed 57000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1280:25600:8536_1:N:0:AATGCCTC+TGGATCGA ptg000076l 137090
Processed 58000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1283:46203:2961_1:N:0:AATGCCTC+TGGATCGA ptg000126l 1
Processed 59000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1283:23254:27167_1:N:0:AATGCCTC+TGGATCGA ptg000109l 39590
Processed 60000000 sequence pairs so far
Processed 61000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1289:18172:8676_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625639
Processed 62000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1292:42100:18384_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625625
Processed 63000000 sequence pairs so far
Processed 64000000 sequence pairs so far
Processed 65000000 sequence pairs so far
Processed 66000000 sequence pairs so far
Processed 67000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1310:3112:15806_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625603
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1311:49966:18944_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625658
Processed 68000000 sequence pairs so far
Processed 69000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1318:26134:6491_1:N:0:AATGCCTC+TGGATCGA ptg000002l 1
Processed 70000000 sequence pairs so far
Processed 71000000 sequence pairs so far
Processed 72000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1326:4860:18916_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625571
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1328:41445:26886_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625574
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1328:41453:26900_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625574
Processed 74000000 sequence pairs so far
Processed 75000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1336:33086:18944_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Processed 76000000 sequence pairs so far
Processed 77000000 sequence pairs so far
Processed 78000000 sequence pairs so far
Processed 79000000 sequence pairs so far
Processed 80000000 sequence pairs so far
Processed 81000000 sequence pairs so far
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1357:7870:16787_1:N:0:AATGTCTC+TGGATCGA ptg000122l 1
Processed 83000000 sequence pairs so far
Processed 84000000 sequence pairs so far
Processed 85000000 sequence pairs so far
Processed 86000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1368:22898:27195_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Processed 87000000 sequence pairs so far
Processed 88000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1375:12143:6645_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625625
Processed 89000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1379:14741:5482_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625634
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1379:50492:23356_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Processed 90000000 sequence pairs so far
Processed 91000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1385:27980:4978_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625639
Processed 92000000 sequence pairs so far
Processed 93000000 sequence pairs so far
Processed 94000000 sequence pairs so far
Processed 95000000 sequence pairs so far
Processed 96000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:26013:22782_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625657
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:36153:24673_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625594
Processed 97000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1403:12985:13621_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:28352:13719_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625641
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1405:13923:9054_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625613
Processed 98000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:19895:12837_1:N:0:AATGTCTC+TGGATCGA ptg000093l 1
Processed 99000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1410:45985:1350_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625663
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1410:45977:1364_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625663
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1412:36784:4110_1:N:0:AATGCCTC+TGGATCGA ptg000113l 1
Processed 100000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1413:19491:12837_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1414:11997:4712_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625612
Processed 101000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1416:6600:7724_1:N:0:AATGTCTC+TGGATCGA ptg000024l 2
Processed 102000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1419:26523:5370_1:N:0:AATGCCTT+TGGATCGA ptg000007l 12295846
Processed 103000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1423:19151:15022_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625582
Processed 104000000 sequence pairs so far
Processed 105000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1429:7199:5258_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625608
Processed 106000000 sequence pairs so far
Processed 107000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1436:27931:12542_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625618
Processed 108000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1438:3994:7163_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625633
Processed 109000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1440:47636:27125_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1441:48380:14658_1:N:0:AATGCCTC+TGGATCGA ptg000109l 39590
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1442:44026:2471_1:N:0:AATGTCTC+TGAATCGA ptg000033l 2625611
Processed 110000000 sequence pairs so far
Processed 111000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1446:11140:19672_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625578
Processed 112000000 sequence pairs so far
Processed 113000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1453:38499:5567_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625577
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1453:24565:6715_1:N:0:AATGCCTC+TGGATCGA ptg000069l 259766
Processed 114000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1458:47166:5440_1:N:0:AATGTCTC+TGGATCGA ptg000039l 3
Processed 115000000 sequence pairs so far
Processed 116000000 sequence pairs so far
Processed 117000000 sequence pairs so far
Processed 118000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1468:21490:5931_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1469:32163:1770_1:N:0:AATGTCTC+TGGATCGA ptg000002l 1
Processed 119000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1470:51139:7500_1:N:0:AATGCCTC+TGGATCGA ptg000019l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1471:16667:27195_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625577
Processed 120000000 sequence pairs so far
Processed 121000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1476:16027:3115_1:N:0:AATGTCTC+TGGATCGA ptg000140l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1476:30998:23314_1:N:0:AATGTCTC+TGGATCGA ptg000025l 21443054
Processed 122000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1479:2732:6939_1:N:0:AATGGCTC+TGGATCGA ptg000046l 39546
Processed 123000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1481:51415:20527_1:N:0:AATGCCTA+TGGATCGA ptg000033l 2625661
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1483:33134:1098_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625592
Processed 124000000 sequence pairs so far
Processed 125000000 sequence pairs so far
Processed 126000000 sequence pairs so far
Processed 127000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1492:2311:26326_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625625
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1492:46009:27082_1:N:0:AGTGCCTC+TGGATCGA ptg000033l 2625588
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1494:49044:10035_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625628
Processed 128000000 sequence pairs so far
Processed 129000000 sequence pairs so far
Processed 130000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2104:51042:9209_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625624
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2106:48024:10483_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625628
Processed 131000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2109:29889:4698_1:N:0:AATGTCTC+TGGATCGA ptg000122l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2109:15793:18566_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 132000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2113:20559:10791_1:N:0:AATGTCTC+TGGATCGA ptg000082l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2113:40353:10904_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
Processed 133000000 sequence pairs so far
Processed 134000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2121:22469:17683_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625624
Processed 135000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2124:5192:28932_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625617
Processed 136000000 sequence pairs so far
Processed 137000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2128:12022:22096_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625589
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2131:39697:9405_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625638
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2131:39713:9405_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625638
Processed 138000000 sequence pairs so far
Processed 139000000 sequence pairs so far
Processed 140000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2138:31427:16773_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625571
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2140:44067:1532_1:N:0:AATGTCTC+TGGATCGA ptg000025l 21443056
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:12879:1812_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625624
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:10088:7878_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625594
Processed 141000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2144:27696:1238_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625573
Processed 142000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2146:49270:8214_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625586
Processed 143000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2149:40603:10245_1:N:0:AATGTCTC+TGGATCGA ptg000090l 1
Processed 144000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2154:7126:4320_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625571
Processed 145000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2154:34380:24211_1:N:0:AATGTCTC+TGGATCGA ptg000132l 1
Processed 146000000 sequence pairs so far
Processed 147000000 sequence pairs so far
Processed 148000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2164:42473:9419_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625611
Processed 149000000 sequence pairs so far
Processed 150000000 sequence pairs so far
Processed 151000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2172:19572:15386_1:N:0:AATGCCTC+TGGATCGA ptg000146l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2172:19564:15400_1:N:0:AATGCCTC+TGGATCGA ptg000146l 1
Processed 152000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2175:26434:20877_1:N:0:AATGGCTC+TGGATCGA ptg000007l 12295882
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2176:42473:6421_1:N:0:AATGCCTC+TGGATCGA ptg000140l 2
Processed 153000000 sequence pairs so far
Processed 154000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2178:3153:29576_1:N:0:AATGGCTC+NGGATCGA ptg000033l 2625652
Processed 155000000 sequence pairs so far
Processed 156000000 sequence pairs so far
Processed 157000000 sequence pairs so far
Processed 158000000 sequence pairs so far
Processed 159000000 sequence pairs so far
Processed 160000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2196:26693:22390_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625590
Processed 161000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2202:19264:24883_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625585
Processed 162000000 sequence pairs so far
Processed 163000000 sequence pairs so far
Processed 164000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2212:47085:16787_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625630
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2213:13988:5104_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625625
Processed 165000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2214:27057:18174_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625613
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2214:42117:29590_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625615
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2217:42376:3535_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 166000000 sequence pairs so far
Processed 167000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2221:13090:1392_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:40361:27615_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:40369:27629_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625572
Processed 168000000 sequence pairs so far
Processed 169000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2229:14708:5006_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625575
Processed 170000000 sequence pairs so far
Processed 171000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:28554:29114_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625617
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:28570:29114_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625617
Processed 172000000 sequence pairs so far
Processed 173000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2242:32972:29338_1:N:0:AATGTCTC+TGGATCGA ptg000008l 38432960
Processed 174000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2244:34097:13271_1:N:0:AATGTCTC+TGGATCGA ptg000023l 3
Processed 175000000 sequence pairs so far
Processed 176000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2252:33150:4432_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625616
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2252:33167:4432_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625616
Processed 177000000 sequence pairs so far
Processed 178000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2256:24306:1448_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625628
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2256:24298:1462_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625628
Processed 179000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2260:37423:29702_1:N:0:AATGTCTC+NGGATCGA ptg000033l 2625621
Processed 180000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2263:37423:19112_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625625
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2263:27866:19490_1:N:0:AATGTCTC+TGGATCGA ptg000146l 1
Processed 181000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2266:43031:2961_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625622
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2267:44528:21942_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625622
Processed 182000000 sequence pairs so far
Processed 183000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2273:31661:1658_1:N:0:AATGCCTC+AGGATCGA ptg000033l 2625577
Processed 184000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2274:27907:1434_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625574
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2275:14368:12010_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625652
Processed 185000000 sequence pairs so far
Processed 186000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2279:50719:29044_1:N:0:AATGCCTC+TGGATCGA ptg000183l 26177
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2279:21401:29562_1:N:0:AATGTCTC+TGGATCGA ptg000093l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2279:21392:29576_1:N:0:AATGTCTC+TGGATCGA ptg000093l 1
Processed 187000000 sequence pairs so far
Processed 188000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2288:25956:6351_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 189000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2290:3177:1714_1:N:0:AATGTCTC+TGGATCGA ptg000036l 6407221
Processed 190000000 sequence pairs so far
Processed 191000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2296:28222:10609_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625621
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2298:41226:8242_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625589
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2298:11601:10301_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625659
Processed 192000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2302:43015:20023_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625639
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2303:3015:20121_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2304:34567:24869_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625573
Processed 193000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2305:5823:18398_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625588
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2305:35368:20317_1:N:0:AATGTCTC+TGGATCGA ptg000066l 66364
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2306:5354:11142_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625613
Processed 194000000 sequence pairs so far
Processed 195000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2314:12774:7346_1:N:0:AATGACTC+TGGATCGA ptg000126l 1
Processed 196000000 sequence pairs so far
Processed 197000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2322:18851:23889_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625613
Processed 198000000 sequence pairs so far
Processed 199000000 sequence pairs so far
Processed 200000000 sequence pairs so far
Processed 201000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2333:4399:19210_1:N:0:AATGTCTC+TGGATCGA ptg000093l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2335:31459:9741_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625574
Processed 202000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2337:26094:11800_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625639
Processed 203000000 sequence pairs so far
Processed 204000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2345:2481:13873_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625667
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2345:2489:13887_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625667
Processed 205000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2346:6640:7374_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625624
Processed 206000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2350:19936:6155_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625613
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2350:19952:6155_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625613
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2350:19928:6169_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625613
Processed 207000000 sequence pairs so far
Processed 208000000 sequence pairs so far
Processed 209000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2357:42206:19854_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2358:25738:2975_1:N:0:AATGCCTC+TGGATCGA ptg000082l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2360:13850:9629_1:N:0:AATGACTC+TGGATCGA ptg000033l 2625577
Processed 210000000 sequence pairs so far
Processed 211000000 sequence pairs so far
Processed 212000000 sequence pairs so far
Processed 213000000 sequence pairs so far
Processed 214000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2374:42821:10609_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625657
Processed 215000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2377:38240:9068_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625571
Processed 216000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2379:42278:21353_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625638
Processed 217000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2383:18593:28595_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625633
Processed 218000000 sequence pairs so far
Processed 219000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2388:29954:19911_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625583
Processed 220000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2391:5726:5286_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2392:8849:24561_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 221000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2397:33061:5763_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625571
Processed 222000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2397:12556:22096_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2398:48874:13243_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625616
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2398:16650:25233_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Processed 223000000 sequence pairs so far
Processed 224000000 sequence pairs so far
Processed 225000000 sequence pairs so far
Processed 226000000 sequence pairs so far
Processed 227000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2419:39932:14321_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625625
Processed 228000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2420:24662:27867_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625611
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2422:3250:21087_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625572
Processed 229000000 sequence pairs so far
Processed 230000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2430:23561:25346_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625592
Processed 231000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2432:35635:1476_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625627
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2434:6098:3774_1:N:0:AATGTCTC+TGGATCGA ptg000025l 21443074
Processed 232000000 sequence pairs so far
Processed 233000000 sequence pairs so far
Processed 234000000 sequence pairs so far
Processed 235000000 sequence pairs so far
Processed 236000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2448:12175:13761_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625575
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2449:13235:1140_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625621
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2449:41348:19238_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2450:11366:6029_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625611
Processed 237000000 sequence pairs so far
Processed 238000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2454:2586:5482_1:N:0:AATGGCTC+TGGATCGA ptg000033l 2625596
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2456:29169:17235_1:N:0:AATGTCTC+TGGATCGA ptg000007l 12295916
Processed 239000000 sequence pairs so far
253975571 reads; of these:
253975571 (100.00%) were paired; of these:
196506494 (77.37%) aligned concordantly 0 times
19124692 (7.53%) aligned concordantly exactly 1 time
38344385 (15.10%) aligned concordantly >1 times
22.63% overall alignment rate
253975571 reads; of these:
253975571 (100.00%) were paired; of these:
196503759 (77.37%) aligned concordantly 0 times
19106380 (7.52%) aligned concordantly exactly 1 time
38365432 (15.11%) aligned concordantly >1 times
22.63% overall alignment rate
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2459:22849:10497_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625578
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2459:1834:22026_1:N:0:AATGTCTC+TGGATCGA ptg000146l 1
Processed 240000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:31572:14924_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625658
Processed 241000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2463:22841:8242_1:N:0:AATGTCTC+TGGATCGA ptg000088l 96907
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2463:22849:8256_1:N:0:AATGTCTC+TGGATCGA ptg000088l 96907
Processed 242000000 sequence pairs so far
253975571 reads; of these:
253975571 (100.00%) were paired; of these:
171431997 (67.50%) aligned concordantly 0 times
27091549 (10.67%) aligned concordantly exactly 1 time
55452025 (21.83%) aligned concordantly >1 times
32.50% overall alignment rate
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2466:16003:21844_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625573
Processed 243000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2468:51520:12192_1:N:0:AATGCCTC+TGGATCGA ptg000033l 2625572
253975571 reads; of these:
253975571 (100.00%) were paired; of these:
171497491 (67.53%) aligned concordantly 0 times
27066203 (10.66%) aligned concordantly exactly 1 time
55411877 (21.82%) aligned concordantly >1 times
32.47% overall alignment rate
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2469:14020:27993_1:N:0:AATGTCTC+TGGATCGA ptg000155l 3
Processed 244000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2473:13559:3998_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625579
Processed 245000000 sequence pairs so far
Processed 246000000 sequence pairs so far
Processed 247000000 sequence pairs so far
Processed 248000000 sequence pairs so far
Processed 249000000 sequence pairs so far
Processed 250000000 sequence pairs so far
Processed 251000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2489:8615:22390_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625634
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2490:10355:27727_1:N:0:AATGTCTC+TGGATCAA ptg000033l 2625618
Processed 252000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2493:22987:26956_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:11601:9125_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:38079:13467_1:N:0:AATGTCTC+TGGATCGA ptg000033l 2625617
Processed 253000000 sequence pairs so far
Processed 253975571 sequences in total
Successfully deleted the temporary files trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-140-TP2_S5_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-140-TP2_S5_R2_001.fastq.gz_G_to_A.fastq
Final Alignment report
======================
Sequence pairs analysed in total: 253975571
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 5587802285
Total methylated C's in CpG context: 98818956
Total methylated C's in CHG context: 18036512
Total methylated C's in CHH context: 87165516
Total methylated C's in Unknown context: 16505398
Total unmethylated C's in CpG context: 857492373
Total unmethylated C's in CHG context: 1013978029
Total unmethylated C's in CHH context: 3512310899
Total unmethylated C's in Unknown context: 62100765
C methylated in CpG context: 10.3%
C methylated in CHG context: 1.7%
C methylated in CHH context: 2.4%
C methylated in unknown context (CN or CHN): 21.0%
Bismark completed in 1d 9h 59m 58s
====================
Bismark run complete
====================