Running Bismark with score_min=L,0,-0.8 Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools' Reference genome folder provided is ../data/ (absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/data/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/code'): ../data/Raw_WGBS_Mch/LCo_BSr1_R1.fastq ../data/Raw_WGBS_Mch/LCo_BSr1_R2.fastq Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/output/02-gallo-align/gallo-out2_L_0_-0.8/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.8 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/code Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/data/ chr OZ263145.1 (133122103 bp) chr OZ263146.1 (115872679 bp) chr OZ263147.1 (112047329 bp) chr OZ263148.1 (104860103 bp) chr OZ263149.1 (102992780 bp) chr OZ263150.1 (102858672 bp) chr OZ263151.1 (98048912 bp) chr OZ263152.1 (97139405 bp) chr OZ263153.1 (94721750 bp) chr OZ263154.1 (91363364 bp) chr OZ263155.1 (86550376 bp) chr OZ263156.1 (81349889 bp) chr OZ263157.1 (74365144 bp) chr OZ263158.1 (73464853 bp) chr CBDTTG010000001.1 (267333 bp) chr CBDTTG010000002.1 (245216 bp) chr CBDTTG010000003.1 (225351 bp) chr CBDTTG010000004.1 (219641 bp) chr CBDTTG010000005.1 (218316 bp) chr CBDTTG010000006.1 (195018 bp) chr CBDTTG010000007.1 (186199 bp) chr CBDTTG010000008.1 (182790 bp) chr CBDTTG010000009.1 (171464 bp) chr CBDTTG010000010.1 (164758 bp) chr CBDTTG010000011.1 (153732 bp) chr CBDTTG010000012.1 (136734 bp) chr CBDTTG010000013.1 (131488 bp) chr CBDTTG010000014.1 (131459 bp) chr CBDTTG010000015.1 (128680 bp) chr CBDTTG010000016.1 (125125 bp) chr CBDTTG010000017.1 (119736 bp) chr CBDTTG010000018.1 (118975 bp) chr CBDTTG010000019.1 (118844 bp) chr CBDTTG010000020.1 (115480 bp) chr CBDTTG010000021.1 (110021 bp) chr CBDTTG010000022.1 (109580 bp) chr CBDTTG010000023.1 (109005 bp) chr CBDTTG010000024.1 (107994 bp) chr CBDTTG010000025.1 (107798 bp) chr CBDTTG010000026.1 (107390 bp) chr CBDTTG010000027.1 (107000 bp) chr CBDTTG010000028.1 (104336 bp) chr CBDTTG010000029.1 (103654 bp) chr CBDTTG010000030.1 (102405 bp) chr CBDTTG010000031.1 (100623 bp) chr CBDTTG010000032.1 (100260 bp) chr CBDTTG010000033.1 (100216 bp) chr CBDTTG010000034.1 (97259 bp) chr CBDTTG010000035.1 (95021 bp) chr CBDTTG010000036.1 (94763 bp) chr CBDTTG010000037.1 (93201 bp) chr CBDTTG010000038.1 (92560 bp) chr CBDTTG010000039.1 (91770 bp) chr CBDTTG010000040.1 (91760 bp) chr CBDTTG010000041.1 (90742 bp) chr CBDTTG010000042.1 (90595 bp) chr CBDTTG010000043.1 (88338 bp) chr CBDTTG010000044.1 (87948 bp) chr CBDTTG010000045.1 (87133 bp) chr CBDTTG010000046.1 (85132 bp) chr CBDTTG010000047.1 (84625 bp) chr CBDTTG010000048.1 (84204 bp) chr CBDTTG010000049.1 (83114 bp) chr CBDTTG010000050.1 (82758 bp) chr CBDTTG010000051.1 (82611 bp) chr CBDTTG010000052.1 (81778 bp) chr CBDTTG010000053.1 (81432 bp) chr CBDTTG010000054.1 (81016 bp) chr CBDTTG010000055.1 (81000 bp) chr CBDTTG010000056.1 (80990 bp) chr CBDTTG010000057.1 (80640 bp) chr CBDTTG010000058.1 (79993 bp) chr CBDTTG010000059.1 (79407 bp) chr CBDTTG010000060.1 (79060 bp) chr CBDTTG010000061.1 (78748 bp) chr CBDTTG010000062.1 (78517 bp) chr CBDTTG010000063.1 (78241 bp) chr CBDTTG010000064.1 (77752 bp) chr CBDTTG010000065.1 (76686 bp) chr CBDTTG010000066.1 (75877 bp) chr CBDTTG010000067.1 (74978 bp) chr CBDTTG010000068.1 (73508 bp) chr CBDTTG010000069.1 (72379 bp) chr CBDTTG010000070.1 (72000 bp) chr CBDTTG010000071.1 (71366 bp) chr CBDTTG010000072.1 (70942 bp) chr CBDTTG010000073.1 (69628 bp) chr CBDTTG010000074.1 (68899 bp) chr CBDTTG010000075.1 (67952 bp) chr CBDTTG010000076.1 (67800 bp) chr CBDTTG010000077.1 (66923 bp) chr CBDTTG010000078.1 (66262 bp) chr CBDTTG010000079.1 (64570 bp) chr CBDTTG010000080.1 (64124 bp) chr CBDTTG010000081.1 (63984 bp) chr CBDTTG010000082.1 (63875 bp) chr CBDTTG010000083.1 (63639 bp) chr CBDTTG010000084.1 (63541 bp) chr CBDTTG010000085.1 (63484 bp) chr CBDTTG010000086.1 (63000 bp) chr CBDTTG010000087.1 (62908 bp) chr CBDTTG010000088.1 (62849 bp) chr CBDTTG010000089.1 (62837 bp) chr CBDTTG010000090.1 (61239 bp) chr CBDTTG010000091.1 (60752 bp) chr CBDTTG010000092.1 (60248 bp) chr CBDTTG010000093.1 (60185 bp) chr CBDTTG010000094.1 (60048 bp) chr CBDTTG010000095.1 (58000 bp) chr CBDTTG010000096.1 (57695 bp) chr CBDTTG010000097.1 (57519 bp) chr CBDTTG010000098.1 (56983 bp) chr CBDTTG010000099.1 (56789 bp) chr CBDTTG010000100.1 (56459 bp) chr CBDTTG010000101.1 (55146 bp) chr CBDTTG010000102.1 (54787 bp) chr CBDTTG010000103.1 (53904 bp) chr CBDTTG010000104.1 (53860 bp) chr CBDTTG010000105.1 (53511 bp) chr CBDTTG010000106.1 (52844 bp) chr CBDTTG010000107.1 (52046 bp) chr CBDTTG010000108.1 (52000 bp) chr CBDTTG010000109.1 (51879 bp) chr CBDTTG010000110.1 (51812 bp) chr CBDTTG010000111.1 (51565 bp) chr CBDTTG010000112.1 (50868 bp) chr CBDTTG010000113.1 (50624 bp) chr CBDTTG010000114.1 (50604 bp) chr CBDTTG010000115.1 (50000 bp) chr CBDTTG010000116.1 (49166 bp) chr CBDTTG010000117.1 (49158 bp) chr CBDTTG010000118.1 (49092 bp) chr CBDTTG010000119.1 (48758 bp) chr CBDTTG010000120.1 (48592 bp) chr CBDTTG010000121.1 (48330 bp) chr CBDTTG010000122.1 (48251 bp) chr CBDTTG010000123.1 (48233 bp) chr CBDTTG010000124.1 (48103 bp) chr CBDTTG010000125.1 (47830 bp) chr CBDTTG010000126.1 (47318 bp) chr CBDTTG010000127.1 (47086 bp) chr CBDTTG010000128.1 (46926 bp) chr CBDTTG010000129.1 (46381 bp) chr CBDTTG010000130.1 (45757 bp) chr CBDTTG010000131.1 (45626 bp) chr CBDTTG010000132.1 (45623 bp) chr CBDTTG010000133.1 (45440 bp) chr CBDTTG010000134.1 (45167 bp) chr CBDTTG010000135.1 (45078 bp) chr CBDTTG010000136.1 (44617 bp) chr CBDTTG010000137.1 (44284 bp) chr CBDTTG010000138.1 (44240 bp) chr CBDTTG010000139.1 (43980 bp) chr CBDTTG010000140.1 (43944 bp) chr CBDTTG010000141.1 (43728 bp) chr CBDTTG010000142.1 (43520 bp) chr CBDTTG010000143.1 (43434 bp) chr CBDTTG010000144.1 (43400 bp) chr CBDTTG010000145.1 (43332 bp) chr CBDTTG010000146.1 (43175 bp) chr CBDTTG010000147.1 (42347 bp) chr CBDTTG010000148.1 (42279 bp) chr CBDTTG010000149.1 (42199 bp) chr CBDTTG010000150.1 (41874 bp) chr CBDTTG010000151.1 (41794 bp) chr CBDTTG010000152.1 (41593 bp) chr CBDTTG010000153.1 (41253 bp) chr CBDTTG010000154.1 (40812 bp) chr CBDTTG010000155.1 (40402 bp) chr CBDTTG010000156.1 (40274 bp) chr CBDTTG010000157.1 (40234 bp) chr CBDTTG010000158.1 (39811 bp) chr CBDTTG010000159.1 (39744 bp) chr CBDTTG010000160.1 (39656 bp) chr CBDTTG010000161.1 (39650 bp) chr CBDTTG010000162.1 (39482 bp) chr CBDTTG010000163.1 (39469 bp) chr CBDTTG010000164.1 (39394 bp) chr CBDTTG010000165.1 (39256 bp) chr CBDTTG010000166.1 (39043 bp) chr CBDTTG010000167.1 (39018 bp) chr CBDTTG010000168.1 (38530 bp) chr CBDTTG010000169.1 (38466 bp) chr CBDTTG010000170.1 (38452 bp) chr CBDTTG010000171.1 (38429 bp) chr CBDTTG010000172.1 (38104 bp) chr CBDTTG010000173.1 (37857 bp) chr CBDTTG010000174.1 (37758 bp) chr CBDTTG010000175.1 (37662 bp) chr CBDTTG010000176.1 (37440 bp) chr CBDTTG010000177.1 (37432 bp) chr CBDTTG010000178.1 (37226 bp) chr CBDTTG010000179.1 (37090 bp) chr CBDTTG010000180.1 (37063 bp) chr CBDTTG010000181.1 (36899 bp) chr CBDTTG010000182.1 (36702 bp) chr CBDTTG010000183.1 (36616 bp) chr CBDTTG010000184.1 (36388 bp) chr CBDTTG010000185.1 (36308 bp) chr CBDTTG010000186.1 (36136 bp) chr CBDTTG010000187.1 (36016 bp) chr CBDTTG010000188.1 (35980 bp) chr CBDTTG010000189.1 (35736 bp) chr CBDTTG010000190.1 (35634 bp) chr CBDTTG010000191.1 (35608 bp) chr CBDTTG010000192.1 (35523 bp) chr CBDTTG010000193.1 (35317 bp) chr CBDTTG010000194.1 (35241 bp) chr CBDTTG010000195.1 (34595 bp) chr CBDTTG010000196.1 (34496 bp) chr CBDTTG010000197.1 (34338 bp) chr CBDTTG010000198.1 (34139 bp) chr CBDTTG010000199.1 (33743 bp) chr CBDTTG010000200.1 (33682 bp) chr CBDTTG010000201.1 (33529 bp) chr CBDTTG010000202.1 (33249 bp) chr CBDTTG010000203.1 (33014 bp) chr CBDTTG010000204.1 (32937 bp) chr CBDTTG010000205.1 (32349 bp) chr CBDTTG010000206.1 (32243 bp) chr CBDTTG010000207.1 (32185 bp) chr CBDTTG010000208.1 (31877 bp) chr CBDTTG010000209.1 (31874 bp) chr CBDTTG010000210.1 (31861 bp) chr CBDTTG010000211.1 (31594 bp) chr CBDTTG010000212.1 (31579 bp) chr CBDTTG010000213.1 (31477 bp) chr CBDTTG010000214.1 (31354 bp) chr CBDTTG010000215.1 (31331 bp) chr CBDTTG010000216.1 (31296 bp) chr CBDTTG010000217.1 (31262 bp) chr CBDTTG010000218.1 (31222 bp) chr CBDTTG010000219.1 (31180 bp) chr CBDTTG010000220.1 (31124 bp) chr CBDTTG010000221.1 (30476 bp) chr CBDTTG010000222.1 (30412 bp) chr CBDTTG010000223.1 (30379 bp) chr CBDTTG010000224.1 (30331 bp) chr CBDTTG010000225.1 (30296 bp) chr CBDTTG010000226.1 (30201 bp) chr CBDTTG010000227.1 (29923 bp) chr CBDTTG010000228.1 (29771 bp) chr CBDTTG010000229.1 (29756 bp) chr CBDTTG010000230.1 (29729 bp) chr CBDTTG010000231.1 (29668 bp) chr CBDTTG010000232.1 (29333 bp) chr CBDTTG010000233.1 (29288 bp) chr CBDTTG010000234.1 (29208 bp) chr CBDTTG010000235.1 (28921 bp) chr CBDTTG010000236.1 (28513 bp) chr CBDTTG010000237.1 (28461 bp) chr CBDTTG010000238.1 (28045 bp) chr CBDTTG010000239.1 (28022 bp) chr CBDTTG010000240.1 (27870 bp) chr CBDTTG010000241.1 (27764 bp) chr CBDTTG010000242.1 (27683 bp) chr CBDTTG010000243.1 (27501 bp) chr CBDTTG010000244.1 (27349 bp) chr CBDTTG010000245.1 (27329 bp) chr CBDTTG010000246.1 (27312 bp) chr CBDTTG010000247.1 (27145 bp) chr CBDTTG010000248.1 (27119 bp) chr CBDTTG010000249.1 (27084 bp) chr CBDTTG010000250.1 (26915 bp) chr CBDTTG010000251.1 (26631 bp) chr CBDTTG010000252.1 (26306 bp) chr CBDTTG010000253.1 (26247 bp) chr CBDTTG010000254.1 (25946 bp) chr CBDTTG010000255.1 (25879 bp) chr CBDTTG010000256.1 (25873 bp) chr CBDTTG010000257.1 (25598 bp) chr CBDTTG010000258.1 (25382 bp) chr CBDTTG010000259.1 (25318 bp) chr CBDTTG010000260.1 (25310 bp) chr CBDTTG010000261.1 (25170 bp) chr CBDTTG010000262.1 (24516 bp) chr CBDTTG010000263.1 (23898 bp) chr CBDTTG010000264.1 (23848 bp) chr CBDTTG010000265.1 (23726 bp) chr CBDTTG010000266.1 (22965 bp) chr CBDTTG010000267.1 (22724 bp) chr CBDTTG010000268.1 (22658 bp) chr CBDTTG010000269.1 (22131 bp) chr CBDTTG010000270.1 (21902 bp) chr CBDTTG010000271.1 (21882 bp) chr CBDTTG010000272.1 (21494 bp) chr CBDTTG010000273.1 (21219 bp) chr CBDTTG010000274.1 (20438 bp) chr CBDTTG010000275.1 (20383 bp) chr CBDTTG010000276.1 (20139 bp) chr CBDTTG010000277.1 (20139 bp) chr CBDTTG010000278.1 (19717 bp) chr CBDTTG010000279.1 (19583 bp) chr CBDTTG010000280.1 (19572 bp) chr CBDTTG010000281.1 (19296 bp) chr CBDTTG010000282.1 (18914 bp) chr CBDTTG010000283.1 (18311 bp) chr CBDTTG010000284.1 (18295 bp) chr CBDTTG010000285.1 (18000 bp) chr CBDTTG010000286.1 (17971 bp) chr CBDTTG010000287.1 (17600 bp) chr CBDTTG010000288.1 (17586 bp) chr CBDTTG010000289.1 (17485 bp) chr CBDTTG010000290.1 (17350 bp) chr CBDTTG010000291.1 (16553 bp) chr CBDTTG010000292.1 (15651 bp) chr CBDTTG010000293.1 (15303 bp) chr CBDTTG010000294.1 (15000 bp) chr CBDTTG010000295.1 (14564 bp) chr CBDTTG010000296.1 (14291 bp) chr CBDTTG010000297.1 (13732 bp) chr CBDTTG010000298.1 (13430 bp) chr CBDTTG010000299.1 (13253 bp) chr CBDTTG010000300.1 (12982 bp) chr CBDTTG010000301.1 (12759 bp) chr CBDTTG010000302.1 (11862 bp) chr CBDTTG010000303.1 (11523 bp) chr CBDTTG010000304.1 (10035 bp) chr CBDTTG010000305.1 (9403 bp) chr CBDTTG010000306.1 (8373 bp) chr CBDTTG010000307.1 (7049 bp) chr CBDTTG010000308.1 (6219 bp) chr CBDTTG010000309.1 (6000 bp) chr CBDTTG010000310.1 (5723 bp) chr CBDTTG010000311.1 (5387 bp) chr CBDTTG010000312.1 (3936 bp) chr CBDTTG010000313.1 (3580 bp) chr CBDTTG010000314.1 (3000 bp) chr CBDTTG010000315.1 (3000 bp) chr CBDTTG010000316.1 (3000 bp) chr CBDTTG010000317.1 (2000 bp) chr CBDTTG010000318.1 (1000 bp) chr CBDTTG010000319.1 (1000 bp) chr CBDTTG010000320.1 (1000 bp) chr CBDTTG010000321.1 (1000 bp) chr CBDTTG010000322.1 (1000 bp) chr CBDTTG010000323.1 (1000 bp) chr CBDTTG010000324.1 (1000 bp) chr OZ263159.1 (16744 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../data/Raw_WGBS_Mch/LCo_BSr1_R1.fastq and ../data/Raw_WGBS_Mch/LCo_BSr1_R2.fastq Input files are in FastQ format Processing reads up to sequence no. 100000 from ../data/Raw_WGBS_Mch/LCo_BSr1_R1.fastq Writing a C -> T converted version of the input file LCo_BSr1_R1.fastq to LCo_BSr1_R1.fastq_C_to_T.fastq Created C -> T converted version of the FastQ file LCo_BSr1_R1.fastq (100001 sequences in total) Processing reads up to sequence no. 100000 from ../data/Raw_WGBS_Mch/LCo_BSr1_R2.fastq Writing a G -> A converted version of the input file LCo_BSr1_R2.fastq to LCo_BSr1_R2.fastq_G_to_A.fastq Created G -> A converted version of the FastQ file LCo_BSr1_R2.fastq (100001 sequences in total) Input files are LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-chilean-mussel/data/ with the specified options: -q --score-min L,0,-0.8 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1 77 * 0 0 * * 0 0 NTTGTTTAAAAATATTTGTATATGTATATTGTATATATTTGTATATTTATTAATGTATGTTTGATATATTTTAAAAAAAAATTAAATTTTAATAATTTGGATAGATTATATAAAATTATATGAGTGAAATTTTATTAATATTTAATTTTAA #FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF, YT:Z:UP A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2 141 * 0 0 * * 0 0 NAAAAAAAAAAAAAATACAAAAATTATTTAACCTACAACTAAAAACTATATTCTACAACCAAACTACTTNTATATTTCCAACAATACAAAAATAAATATAAACTTATCATAAAATCAAAAATATTAAAAAAAACTTATTATTAAAATTAAA #FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1 77 * 0 0 * * 0 0 NTTGTTTAAAAATATTTGTATATGTATATTGTATATATTTGTATATTTATTAATGTATGTTTGATATATTTTAAAAAAAAATTAAATTTTAATAATTTGGATAGATTATATAAAATTATATGAGTGAAATTTTATTAATATTTAATTTTAA #FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF, YT:Z:UP A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2 141 * 0 0 * * 0 0 NAAAAAAAAAAAAAATACAAAAATTATTTAACCTACAACTAAAAACTATATTCTACAACCAAACTACTTNTATATTTCCAACAATACAAAAATAAATATAAACTTATCATAAAATCAAAAATATTAAAAAAAACTTATTATTAAAATTAAA #FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to LCo_BSr1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/Raw_WGBS_Mch/LCo_BSr1_R1.fastq and ../data/Raw_WGBS_Mch/LCo_BSr1_R2.fastq 100000 reads; of these: 100000 (100.00%) were paired; of these: 55170 (55.17%) aligned concordantly 0 times 15612 (15.61%) aligned concordantly exactly 1 time 29218 (29.22%) aligned concordantly >1 times 44.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 55168 (55.17%) aligned concordantly 0 times 15564 (15.56%) aligned concordantly exactly 1 time 29268 (29.27%) aligned concordantly >1 times 44.83% overall alignment rate Processed 100000 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 400004. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 400004. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 400004. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 400004. Successfully deleted the temporary files LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 50005 Mapping efficiency: 50.0% Sequence pairs with no alignments under any condition: 39345 Sequence pairs did not map uniquely: 10650 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 24936 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 25069 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2159039 Total methylated C's in CpG context: 38320 Total methylated C's in CHG context: 8628 Total methylated C's in CHH context: 40948 Total methylated C's in Unknown context: 1601 Total unmethylated C's in CpG context: 199030 Total unmethylated C's in CHG context: 330231 Total unmethylated C's in CHH context: 1541882 Total unmethylated C's in Unknown context: 13590 C methylated in CpG context: 16.1% C methylated in CHG context: 2.5% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 10.5% Bismark completed in 0d 0h 0m 46s ==================== Bismark run complete ====================