/var/spool/slurm/d/job1154897/slurm_script: line 21: fg: no job control Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-205_S26_L004_R1_001_val_1.fq.gz to EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-205_S26_L004_R1_001_val_1.fq.gz (16541499 sequences in total) Writing a G -> A converted version of the input file EPI-205_S26_L004_R2_001_val_2.fq.gz to EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-205_S26_L004_R2_001_val_2.fq.gz (16541499 sequences in total) Input files are EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1391:2218_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 GATGTAGGTTGTGGTTGATGGAGAAATATTGGAAGTAGTATTTGT BBBBB/FFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2207:16029:91165_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1307:5697:61464_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1307:15236:74734_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2311:19764:98894_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2312:8469:63141_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2306:20347:27366_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2304:13476:67361_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2213:13737:21109_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2110:4838:55204_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2111:6956:43721_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:14209:22679_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2104:3916:83863_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1210:12994:93064_1:N:0:ATCACG PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:7255:87113_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1308:6575:65426_1:N:0:ATCACG PGA_scaffold10__49_contigs__length_53961475 1 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1205:14615:52110_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1110:9753:67516_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1206:12842:18726_1:N:0:ATCACG PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1206:13498:54218_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1112:9498:37340_1:N:0:ATCACG PGA_scaffold16__33_contigs__length_31980953 2 Processed 16000000 sequence pairs so far 16541499 reads; of these: 16541499 (100.00%) were paired; of these: 10229157 (61.84%) aligned concordantly 0 times 1679934 (10.16%) aligned concordantly exactly 1 time 4632408 (28.00%) aligned concordantly >1 times 38.16% overall alignment rate 16541499 reads; of these: 16541499 (100.00%) were paired; of these: 10158419 (61.41%) aligned concordantly 0 times 1656562 (10.01%) aligned concordantly exactly 1 time 4726518 (28.57%) aligned concordantly >1 times 38.59% overall alignment rate Processed 16541499 sequences in total Successfully deleted the temporary files EPI-205_S26_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-205_S26_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16541499 Number of paired-end alignments with a unique best hit: 7025382 Mapping efficiency: 42.5% Sequence pairs with no alignments under any condition: 8039389 Sequence pairs did not map uniquely: 1476728 Sequence pairs which were discarded because genomic sequence could not be extracted: 20 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3423867 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3601495 ((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: 203655615 Total methylated C's in CpG context: 7398519 Total methylated C's in CHG context: 1161571 Total methylated C's in CHH context: 4560293 Total methylated C's in Unknown context: 178365 Total unmethylated C's in CpG context: 22754525 Total unmethylated C's in CHG context: 43791734 Total unmethylated C's in CHH context: 123988973 Total unmethylated C's in Unknown context: 1416101 C methylated in CpG context: 24.5% C methylated in CHG context: 2.6% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 1h 10m 3s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-206_S27_L004_R1_001_val_1.fq.gz to EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-206_S27_L004_R1_001_val_1.fq.gz (20931018 sequences in total) Writing a G -> A converted version of the input file EPI-206_S27_L004_R2_001_val_2.fq.gz to EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-206_S27_L004_R2_001_val_2.fq.gz (20931018 sequences in total) Input files are EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1645:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 TTATATGAGGTGGTGGTTATATTTTGATTTAATTTGAGGTTTTTTTTATTAATATGATTGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF>> Writing bisulfite mapping results to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2115:2003:45527_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1315:12771:97030_1:N:0:CGATGT PGA_scaffold10__49_contigs__length_53961475 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1115:16005:65158_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2310:12960:10687_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2213:13266:29289_1:N:0:CGATGT PGA_scaffold10__49_contigs__length_53961475 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2110:21329:82012_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2204:20423:85884_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2102:12227:18905_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2206:13965:56240_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2112:6898:90793_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:6353:16906_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1316:5541:34408_1:N:0:CTATGT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1316:14816:41240_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:2892:22642_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:14006:58140_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1304:6735:68283_1:N:0:CGATGT PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1306:17684:2470_1:N:0:CGATGT PGA_scaffold10__49_contigs__length_53961475 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1205:6412:68423_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1110:20321:66555_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 2 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1102:9884:77591_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1104:7449:28621_1:N:0:CGATGT PGA_scaffold16__33_contigs__length_31980953 1 20931018 reads; of these: 20931018 (100.00%) were paired; of these: 12014284 (57.40%) aligned concordantly 0 times 2288031 (10.93%) aligned concordantly exactly 1 time 6628703 (31.67%) aligned concordantly >1 times 42.60% overall alignment rate 20931018 reads; of these: 20931018 (100.00%) were paired; of these: 12137090 (57.99%) aligned concordantly 0 times 2314934 (11.06%) aligned concordantly exactly 1 time 6478994 (30.95%) aligned concordantly >1 times 42.01% overall alignment rate Processed 20931018 sequences in total Successfully deleted the temporary files EPI-206_S27_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-206_S27_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 20931018 Number of paired-end alignments with a unique best hit: 9918260 Mapping efficiency: 47.4% Sequence pairs with no alignments under any condition: 9026731 Sequence pairs did not map uniquely: 1986027 Sequence pairs which were discarded because genomic sequence could not be extracted: 21 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4828301 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5089938 ((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: 296793855 Total methylated C's in CpG context: 10485331 Total methylated C's in CHG context: 1669822 Total methylated C's in CHH context: 6970670 Total methylated C's in Unknown context: 260875 Total unmethylated C's in CpG context: 32893020 Total unmethylated C's in CHG context: 64524289 Total unmethylated C's in CHH context: 180250723 Total unmethylated C's in Unknown context: 1999481 C methylated in CpG context: 24.2% C methylated in CHG context: 2.5% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 11.5% Bismark completed in 0d 1h 36m 37s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-214_S30_L004_R1_001_val_1.fq.gz to EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-214_S30_L004_R1_001_val_1.fq.gz (28660043 sequences in total) Writing a G -> A converted version of the input file EPI-214_S30_L004_R2_001_val_2.fq.gz to EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-214_S30_L004_R2_001_val_2.fq.gz (28660043 sequences in total) Input files are EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1228:2242_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAAGATGTATTTTTATAGTATAATGAAGTATATTTATTTTT BBBBBFFFFFFFFFFFFFFFFBBFFBFFFFFFFFFBFFFFF YT:Z:UP D00743:144:CAAWNANXX:4:2315:1228:2242_2:N:0:ACAGTG/2 141 * 0 0 * * 0 0 AAAAATAAATATACTTCATTATACTATAAAAATACATCTTA BBBFFFFFBF>> Writing bisulfite mapping results to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2307:21282:95127_1:N:0:ACAGTG PGA_scaffold9__45_contigs__length_38581958 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1107:4273:84116_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2301:15902:54945_1:N:0:ACAGTG PGA_scaffold10__49_contigs__length_53961475 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2302:8005:16451_1:N:0:ACAGTG PGA_scaffold9__45_contigs__length_38581958 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2302:6720:39327_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2213:12117:7467_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 1 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:1731:5675_1:N:0:ACAGTG PGA_scaffold10__49_contigs__length_53961475 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:3351:47941_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1212:2086:95082_1:N:0:ACAGTG PGA_scaffold10__49_contigs__length_53961475 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1109:11354:68408_1:N:0:ACAGTG PGA_scaffold9__45_contigs__length_38581958 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1113:14438:14193_1:N:0:ACAGTG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1113:11992:87681_1:N:0:ACAGTG PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1102:11223:82484_1:N:0:ACAGTG PGA_scaffold10__49_contigs__length_53961475 1 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 D00743:144:CAAWNANXX:4:1106:11751:57911_1:N:0:ACAGTG PGA_scaffold9__45_contigs__length_38581958 1 28660043 reads; of these: 28660043 (100.00%) were paired; of these: 16476782 (57.49%) aligned concordantly 0 times 3324068 (11.60%) aligned concordantly exactly 1 time 8859193 (30.91%) aligned concordantly >1 times 42.51% overall alignment rate 28660043 reads; of these: 28660043 (100.00%) were paired; of these: 16406980 (57.25%) aligned concordantly 0 times 3283248 (11.46%) aligned concordantly exactly 1 time 8969815 (31.30%) aligned concordantly >1 times 42.75% overall alignment rate Processed 28660043 sequences in total Successfully deleted the temporary files EPI-214_S30_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-214_S30_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28660043 Number of paired-end alignments with a unique best hit: 13828654 Mapping efficiency: 48.3% Sequence pairs with no alignments under any condition: 12337643 Sequence pairs did not map uniquely: 2493746 Sequence pairs which were discarded because genomic sequence could not be extracted: 14 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6750401 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 7078239 ((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: 426052941 Total methylated C's in CpG context: 13963490 Total methylated C's in CHG context: 2165482 Total methylated C's in CHH context: 8555313 Total methylated C's in Unknown context: 307555 Total unmethylated C's in CpG context: 46626860 Total unmethylated C's in CHG context: 90587401 Total unmethylated C's in CHH context: 264154395 Total unmethylated C's in Unknown context: 2806908 C methylated in CpG context: 23.0% C methylated in CHG context: 2.3% C methylated in CHH context: 3.1% C methylated in unknown context (CN or CHN): 9.9% Bismark completed in 0d 2h 16m 13s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-215_S31_L004_R1_001_val_1.fq.gz to EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-215_S31_L004_R1_001_val_1.fq.gz (21150005 sequences in total) Writing a G -> A converted version of the input file EPI-215_S31_L004_R2_001_val_2.fq.gz to EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-215_S31_L004_R2_001_val_2.fq.gz (21150005 sequences in total) Input files are EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1539:2240_1:N:0:GCCAAT/1 99 PGA_scaffold13__52_contigs__length_44396874_CT_converted 10986795 1 101M = 10986886 190 ATGGTAGTAGAGTGTTGGATTAATATTGGGGTTTGTATGTTTGAGTGTATGGTTTAGTAGTAGAGTGTTGGATTAATATTGGGGGTTGTATGTTTGAGTGT BBBBBFF>> Writing bisulfite mapping results to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2215:5479:86150_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1315:7722:97948_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1215:9864:47236_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2312:16018:101277_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2305:14171:2484_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2308:6180:34289_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2213:19532:85548_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2202:4445:85382_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2208:6685:32992_1:N:0:GCCAAT PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2111:2945:8269_1:N:0:TCCAAT PGA_scaffold16__33_contigs__length_31980953 1 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 D00743:144:CAAWNANXX:4:2105:8315:51707_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1309:1222:75964_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2104:16853:40815_1:N:0:GCCAAT PGA_scaffold10__49_contigs__length_53961475 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2108:11087:18700_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 2 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1210:15534:78264_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:5400:80867_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1211:2836:14808_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1213:5661:69678_1:N:0:GCCAAT PGA_scaffold10__49_contigs__length_53961475 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1212:8710:34732_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1110:6134:17618_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1110:11317:68293_1:N:0:GCTAAT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1214:5792:34060_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1214:17972:92900_1:N:0:GCCAAT PGA_scaffold10__49_contigs__length_53961475 1 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1108:1899:71769_1:N:0:GCCAAT PGA_scaffold16__33_contigs__length_31980953 1 Processed 21000000 sequence pairs so far 21150005 reads; of these: 21150005 (100.00%) were paired; of these: 2115000512007518 reads; of these: ( 56.77 %21150005) aligned concordantly 0 times ( 2449025 (11.58%100.00) aligned concordantly exactly 1 time% ) were paired; of these: 6693462 (1211083731.65 (%57.26) aligned concordantly >1 times% ) aligned concordantly 0 times43.23 % overall alignment rate2481177 (11.73%) aligned concordantly exactly 1 time 6557991 (31.01%) aligned concordantly >1 times 42.74% overall alignment rate Processed 21150005 sequences in total Successfully deleted the temporary files EPI-215_S31_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-215_S31_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 21150005 Number of paired-end alignments with a unique best hit: 10236960 Mapping efficiency: 48.4% Sequence pairs with no alignments under any condition: 8937067 Sequence pairs did not map uniquely: 1975978 Sequence pairs which were discarded because genomic sequence could not be extracted: 24 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4997699 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5239237 ((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: 306752449 Total methylated C's in CpG context: 11752174 Total methylated C's in CHG context: 1777591 Total methylated C's in CHH context: 7279068 Total methylated C's in Unknown context: 275365 Total unmethylated C's in CpG context: 31866501 Total unmethylated C's in CHG context: 65426912 Total unmethylated C's in CHH context: 188650203 Total unmethylated C's in Unknown context: 2057640 C methylated in CpG context: 26.9% C methylated in CHG context: 2.6% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 11.8% Bismark completed in 0d 1h 39m 55s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-220_S32_L004_R1_001_val_1.fq.gz to EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-220_S32_L004_R1_001_val_1.fq.gz (15670592 sequences in total) Writing a G -> A converted version of the input file EPI-220_S32_L004_R2_001_val_2.fq.gz to EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-220_S32_L004_R2_001_val_2.fq.gz (15670592 sequences in total) Input files are EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1490:2220_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTTTTTGGTTGTTGTATGGTGTTGTTGTATAGTGTTGTGGTGTTGTTGTATGGTGTTGGTATATGGTGTTGTGGTGTTATGTATGGTGTTGTGGTGTTGGT BBBBBFFFFFFBFFFFFFF/BFFFFFBF/FFFFFFFFFFFBF>> Writing bisulfite mapping results to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2307:12973:60077_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2115:16081:69519_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2107:10414:38246_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1207:8286:85897_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2312:2739:4970_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2308:5116:40102_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2209:3298:13787_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2212:14927:92784_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2110:8429:25160_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2113:7507:30650_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2101:6262:24449_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2116:14308:81928_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2105:7023:87389_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2104:13611:17370_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 1 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1316:15627:43850_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:6853:52957_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1112:21316:50129_1:N:0:CAGATC PGA_scaffold16__33_contigs__length_31980953 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1114:15650:83208_1:N:0:CAGATC PGA_scaffold10__49_contigs__length_53961475 1 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 8753807 (55.86%) aligned concordantly 0 times 1843704 (11.77%) aligned concordantly exactly 1 time 5073081 (32.37%) aligned concordantly >1 times 44.14% overall alignment rate 15670592 reads; of these: 15670592 (100.00%) were paired; of these: 8829468 (56.34%) aligned concordantly 0 times 1870040 (11.93%) aligned concordantly exactly 1 time 4971084 (31.72%) aligned concordantly >1 times 43.66% overall alignment rate Processed 15670592 sequences in total Successfully deleted the temporary files EPI-220_S32_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-220_S32_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 15670592 Number of paired-end alignments with a unique best hit: 7812000 Mapping efficiency: 49.9% Sequence pairs with no alignments under any condition: 6437579 Sequence pairs did not map uniquely: 1421013 Sequence pairs which were discarded because genomic sequence could not be extracted: 18 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3807899 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4004083 ((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: 241180813 Total methylated C's in CpG context: 8360975 Total methylated C's in CHG context: 1444434 Total methylated C's in CHH context: 9329429 Total methylated C's in Unknown context: 348452 Total unmethylated C's in CpG context: 25279896 Total unmethylated C's in CHG context: 50350749 Total unmethylated C's in CHH context: 146415330 Total unmethylated C's in Unknown context: 1649919 C methylated in CpG context: 24.9% C methylated in CHG context: 2.8% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 17.4% Bismark completed in 0d 1h 16m 45s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-221_S33_L004_R1_001_val_1.fq.gz to EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-221_S33_L004_R1_001_val_1.fq.gz (16300374 sequences in total) Writing a G -> A converted version of the input file EPI-221_S33_L004_R2_001_val_2.fq.gz to EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-221_S33_L004_R2_001_val_2.fq.gz (16300374 sequences in total) Input files are EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1412:2190_1:N:0:ACTTGA/1 99 PGA_scaffold13__52_contigs__length_44396874_CT_converted 41856358 6 98M = 41856393 133 ATTTTNTGTTTTATGTTTTATTTTTATTTTAGTGTTTGAAAAAATTTTGGAGAAAGGTAGATATTTTTTAGTGGTTGTAAAAAATATAAGTTGGATTG BBBBB#BBBBFFFFFFFFFFFFFFFFFFFFFBF7FFFFF>> Writing bisulfite mapping results to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2315:2427:24731_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2310:12678:93385_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2310:4534:98852_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2211:12724:10197_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2203:12713:34706_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2214:18153:34718_1:N:0:ACTTGA PGA_scaffold10__49_contigs__length_53961475 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2208:10673:83520_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2208:16057:93463_1:N:0:ACTTGA PGA_scaffold10__49_contigs__length_53961475 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2113:21123:15538_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2102:19504:87938_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2112:15520:57996_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2103:13364:91695_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2114:8146:57499_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1311:3331:89016_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1303:5045:11920_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 2 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:8130:74883_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1104:12778:79637_1:N:0:ACTTGA PGA_scaffold10__49_contigs__length_53961475 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1106:3691:98179_1:N:0:ACTTGA PGA_scaffold16__33_contigs__length_31980953 1 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 9319090 (57.17%) aligned concordantly 0 times 1895297 (11.63%) aligned concordantly exactly 1 time 5085987 (31.20%) aligned concordantly >1 times 42.83% overall alignment rate 16300374 reads; of these: 16300374 (100.00%) were paired; of these: 9257305 (56.79%) aligned concordantly 0 times 1877958 (11.52%) aligned concordantly exactly 1 time 5165111 (31.69%) aligned concordantly >1 times 43.21% overall alignment rate Processed 16300374 sequences in total Successfully deleted the temporary files EPI-221_S33_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-221_S33_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 16300374 Number of paired-end alignments with a unique best hit: 7892273 Mapping efficiency: 48.4% Sequence pairs with no alignments under any condition: 6884123 Sequence pairs did not map uniquely: 1523978 Sequence pairs which were discarded because genomic sequence could not be extracted: 18 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3864190 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4028065 ((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: 237162640 Total methylated C's in CpG context: 8470434 Total methylated C's in CHG context: 1445513 Total methylated C's in CHH context: 8458428 Total methylated C's in Unknown context: 319697 Total unmethylated C's in CpG context: 24499627 Total unmethylated C's in CHG context: 49584430 Total unmethylated C's in CHH context: 144704208 Total unmethylated C's in Unknown context: 1602248 C methylated in CpG context: 25.7% C methylated in CHG context: 2.8% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 0d 1h 17m 22s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-226_S34_L004_R1_001_val_1.fq.gz to EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-226_S34_L004_R1_001_val_1.fq.gz (11133150 sequences in total) Writing a G -> A converted version of the input file EPI-226_S34_L004_R2_001_val_2.fq.gz to EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-226_S34_L004_R2_001_val_2.fq.gz (11133150 sequences in total) Input files are EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1168:2235_1:N:0:GATCAG/1 99 PGA_scaffold9__45_contigs__length_38581958_CT_converted 21134968 1 84M = 21134968 -84 TTATATTATATTTTATANTGTGTAAAGTTGTNGTTAAGTGATTTATATTTGTNGTATTTTNNTTGTTATTGTTTATATAGTGGG BBBBBFFFFFFFFFFBF#BB>> Writing bisulfite mapping results to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R2_001_val_2.fq.gz Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2107:18931:75989_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2313:13006:82214_1:N:0:GATCAG PGA_scaffold10__49_contigs__length_53961475 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2301:7393:34581_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2303:5939:38997_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2209:20564:96732_1:N:0:GATCAG PGA_scaffold9__45_contigs__length_38581958 3 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2210:8547:64323_1:N:0:GATCAG PGA_scaffold10__49_contigs__length_53961475 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2110:20655:2488_1:N:0:GATCAG PGA_scaffold10__49_contigs__length_53961475 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1309:5639:23929_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1313:20501:6797_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1209:9766:40667_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1304:5768:7180_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1204:20228:97921_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1102:2811:49827_1:N:0:GATCAG PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1112:1877:81911_1:N:0:GATCAG PGA_scaffold10__49_contigs__length_53961475 1 Processed 11000000 sequence pairs so far 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 6103771 (54.83%) aligned concordantly 0 times 1398512 (12.56%) aligned concordantly exactly 1 time 3630867 (32.61%) aligned concordantly >1 times 45.17% overall alignment rate 11133150 reads; of these: 11133150 (100.00%) were paired; of these: 6051307 (54.35%) aligned concordantly 0 times 1377150 (12.37%) aligned concordantly exactly 1 time 3704693 (33.28%) aligned concordantly >1 times 45.65% overall alignment rate Processed 11133150 sequences in total Successfully deleted the temporary files EPI-226_S34_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-226_S34_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 11133150 Number of paired-end alignments with a unique best hit: 5810287 Mapping efficiency: 52.2% Sequence pairs with no alignments under any condition: 4332142 Sequence pairs did not map uniquely: 990721 Sequence pairs which were discarded because genomic sequence could not be extracted: 14 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2836017 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2974256 ((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: 181942001 Total methylated C's in CpG context: 6609078 Total methylated C's in CHG context: 1105118 Total methylated C's in CHH context: 7285387 Total methylated C's in Unknown context: 262752 Total unmethylated C's in CpG context: 18761881 Total unmethylated C's in CHG context: 37898881 Total unmethylated C's in CHH context: 110281656 Total unmethylated C's in Unknown context: 1234674 C methylated in CpG context: 26.0% C methylated in CHG context: 2.8% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 17.5% Bismark completed in 0d 0h 57m 26s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_v074'): /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz 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: /gscratch/scrubbed/strigg/analyses/20190806_v074/ Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_v074 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file EPI-227_S35_L004_R1_001_val_1.fq.gz to EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-227_S35_L004_R1_001_val_1.fq.gz (13531234 sequences in total) Writing a G -> A converted version of the input file EPI-227_S35_L004_R2_001_val_2.fq.gz to EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-227_S35_L004_R2_001_val_2.fq.gz (13531234 sequences in total) Input files are EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:4:2315:1203:2205_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 TTTGTTTTTTTTTATATATAAATTATTAATTAAATAATTTAATTTTGTAAAANTTGTAAAANTATATAAATATTTATGTATTATTTTAATATTTTATAGTT BBBBB>> Writing bisulfite mapping results to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1207:3246:50803_1:N:0:TAGCTT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1115:4854:81263_1:N:0:TAGCTT PGA_scaffold16__33_contigs__length_31980953 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2316:7307:79319_1:N:0:TAGCTT PGA_scaffold10__49_contigs__length_53961475 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2306:20234:5849_1:N:0:TAGCTT PGA_scaffold16__33_contigs__length_31980953 1 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2210:2940:71139_1:N:0:TAGCTT PGA_scaffold10__49_contigs__length_53961475 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2109:4887:55997_1:N:0:TAGCTT PGA_scaffold10__49_contigs__length_53961475 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2104:14781:60566_1:N:0:TAGCTT PGA_scaffold16__33_contigs__length_31980953 2 Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:2108:5417:54747_1:N:0:TAGCTT PGA_scaffold16__33_contigs__length_31980953 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for D00743:144:CAAWNANXX:4:1202:10881:3556_1:N:0:TAGCTT PGA_scaffold10__49_contigs__length_53961475 1 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 7489531 (55.35%) aligned concordantly 0 times 1641888 (12.13%) aligned concordantly exactly 1 time 4399815 (32.52%) aligned concordantly >1 times 44.65% overall alignment rate 13531234 reads; of these: 13531234 (100.00%) were paired; of these: 7450031 (55.06%) aligned concordantly 0 times 1632480 (12.06%) aligned concordantly exactly 1 time 4448723 (32.88%) aligned concordantly >1 times 44.94% overall alignment rate Processed 13531234 sequences in total Successfully deleted the temporary files EPI-227_S35_L004_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-227_S35_L004_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 13531234 Number of paired-end alignments with a unique best hit: 6848677 Mapping efficiency: 50.6% Sequence pairs with no alignments under any condition: 5415876 Sequence pairs did not map uniquely: 1266681 Sequence pairs which were discarded because genomic sequence could not be extracted: 9 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3353489 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3495179 ((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: 209732703 Total methylated C's in CpG context: 7552418 Total methylated C's in CHG context: 1267634 Total methylated C's in CHH context: 8547890 Total methylated C's in Unknown context: 313577 Total unmethylated C's in CpG context: 21092550 Total unmethylated C's in CHG context: 43317740 Total unmethylated C's in CHH context: 127954471 Total unmethylated C's in Unknown context: 1377183 C methylated in CpG context: 26.4% C methylated in CHG context: 2.8% C methylated in CHH context: 6.3% C methylated in unknown context (CN or CHN): 18.5% Bismark completed in 0d 1h 6m 45s ==================== Bismark run complete ==================== /var/spool/slurm/d/job1154897/slurm_script: line 37: fg: no job control Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:PGA_scaffold1__77_contigs__length_89643857 LN:89643857 skipping header line: @SQ SN:PGA_scaffold2__36_contigs__length_69596280 LN:69596280 skipping header line: @SQ SN:PGA_scaffold3__111_contigs__length_57743597 LN:57743597 skipping header line: @SQ SN:PGA_scaffold4__129_contigs__length_65288255 LN:65288255 skipping header line: @SQ SN:PGA_scaffold5__109_contigs__length_67248332 LN:67248332 skipping header line: @SQ SN:PGA_scaffold6__104_contigs__length_61759565 LN:61759565 skipping header line: @SQ SN:PGA_scaffold7__69_contigs__length_43120122 LN:43120122 skipping header line: @SQ SN:PGA_scaffold8__63_contigs__length_61151155 LN:61151155 skipping header line: @SQ SN:PGA_scaffold9__45_contigs__length_38581958 LN:38581958 skipping header line: @SQ SN:PGA_scaffold10__49_contigs__length_53961475 LN:53961475 skipping header line: @SQ SN:PGA_scaffold11__79_contigs__length_51449921 LN:51449921 skipping header line: @SQ SN:PGA_scaffold12__71_contigs__length_50438331 LN:50438331 skipping header line: @SQ SN:PGA_scaffold13__52_contigs__length_44396874 LN:44396874 skipping header line: @SQ SN:PGA_scaffold14__91_contigs__length_45393038 LN:45393038 skipping header line: @SQ SN:PGA_scaffold15__101_contigs__length_47938513 LN:47938513 skipping header line: @SQ SN:PGA_scaffold16__33_contigs__length_31980953 LN:31980953 skipping header line: @SQ SN:PGA_scaffold17__51_contigs__length_34923512 LN:34923512 skipping header line: @SQ SN:PGA_scaffold18__69_contigs__length_27737463 LN:27737463 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074" Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now testing Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam for positional sorting (which would be bad...) /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Found 8 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/Bowtie single-end BAM files detected No Bismark/Bowtie paired-end BAM files detected Generating Bismark summary report from 8 Bismark BAM file(s)... >> Reading from Bismark report: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/strigg/analyses/20190806_v074/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v074/< CX context: no (CpG context only, default) Genome coordinates used: 1-based (default) GZIP compression: yes Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== gzip: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz_R1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz: No such file or directory >>> Writing genome-wide cytosine report to: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz_cytosine_CpG_cov_report.CpG_report.txt.gz <<< No last chromosome was defined, something must have gone wrong while reading the data in (e.g. specified wrong file path for a gzipped coverage file?). Please check your command! xargs: /gscratch/srlab/programs/Bismark-0.19.0/coverage2cytosine: exited with status 255; aborting [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory [E::hts_open_format] Failed to open file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam samtools sort: can't open "/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam_R1_001_bismark_bt2_pe.deduplicated.bam": No such file or directory