/var/spool/slurm/d/job1154933/slurm_script: line 22: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-0.2/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99915 (99.92%) aligned concordantly 0 times
    28 (0.03%) aligned concordantly exactly 1 time
    57 (0.06%) aligned concordantly >1 times
0.09% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99937 (99.94%) aligned concordantly 0 times
    17 (0.02%) aligned concordantly exactly 1 time
    46 (0.05%) aligned concordantly >1 times
0.06% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99930 (99.93%) aligned concordantly 0 times
    26 (0.03%) aligned concordantly exactly 1 time
    44 (0.04%) aligned concordantly >1 times
0.07% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99917 (99.92%) aligned concordantly 0 times
    23 (0.02%) aligned concordantly exactly 1 time
    60 (0.06%) aligned concordantly >1 times
0.08% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	98
Mapping efficiency:	0.1%

Sequence pairs with no alignments under any condition:	99810
Sequence pairs did not map uniquely:	92
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	23	((converted) top strand)
GA/CT/CT:	27	(complementary to (converted) top strand)
GA/CT/GA:	25	(complementary to (converted) bottom strand)
CT/GA/GA:	23	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4241

Total methylated C's in CpG context:	10
Total methylated C's in CHG context:	4
Total methylated C's in CHH context:	22
Total methylated C's in Unknown context:	2

Total unmethylated C's in CpG context:	672
Total unmethylated C's in CHG context:	717
Total unmethylated C's in CHH context:	2816
Total unmethylated C's in Unknown context:	24

C methylated in CpG context:	1.5%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.8%
C methylated in unknown context (CN or CHN):	7.7%


Bismark completed in 0d 0h 0m 30s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-0.2/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99899 (99.90%) aligned concordantly 0 times
    35 (0.04%) aligned concordantly exactly 1 time
    66 (0.07%) aligned concordantly >1 times
0.10% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99918 (99.92%) aligned concordantly 0 times
    20 (0.02%) aligned concordantly exactly 1 time
    62 (0.06%) aligned concordantly >1 times
0.08% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99919 (99.92%) aligned concordantly 0 times
    20 (0.02%) aligned concordantly exactly 1 time
    61 (0.06%) aligned concordantly >1 times
0.08% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99915 (99.92%) aligned concordantly 0 times
    16 (0.02%) aligned concordantly exactly 1 time
    69 (0.07%) aligned concordantly >1 times
0.09% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	105
Mapping efficiency:	0.1%

Sequence pairs with no alignments under any condition:	99787
Sequence pairs did not map uniquely:	108
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	19	((converted) top strand)
GA/CT/CT:	25	(complementary to (converted) top strand)
GA/CT/GA:	27	(complementary to (converted) bottom strand)
CT/GA/GA:	34	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4932

Total methylated C's in CpG context:	3
Total methylated C's in CHG context:	4
Total methylated C's in CHH context:	9
Total methylated C's in Unknown context:	2

Total unmethylated C's in CpG context:	825
Total unmethylated C's in CHG context:	894
Total unmethylated C's in CHH context:	3197
Total unmethylated C's in Unknown context:	30

C methylated in CpG context:	0.4%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.3%
C methylated in unknown context (CN or CHN):	6.2%


Bismark completed in 0d 0h 0m 29s

====================
Bismark run complete
====================

/var/spool/slurm/d/job1154933/slurm_script: line 39: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-0.6/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99808 (99.81%) aligned concordantly 0 times
    45 (0.04%) aligned concordantly exactly 1 time
    147 (0.15%) aligned concordantly >1 times
0.19% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99842 (99.84%) aligned concordantly 0 times
    44100000 ( reads; of these:0.04
%  ) aligned concordantly exactly 1 time100000
 (    114 (100.000.11%%) were paired; of these:) aligned concordantly >1 times

    0.1699814% ( overall alignment rate99.81
%) aligned concordantly 0 times
    41 (0.04%) aligned concordantly exactly 1 time
    145 (0.14%) aligned concordantly >1 times
0.19% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99857 (99.86%) aligned concordantly 0 times
    31 (0.03%) aligned concordantly exactly 1 time
    112 (0.11%) aligned concordantly >1 times
0.14% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	245
Mapping efficiency:	0.2%

Sequence pairs with no alignments under any condition:	99596
Sequence pairs did not map uniquely:	159
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	68	((converted) top strand)
GA/CT/CT:	59	(complementary to (converted) top strand)
GA/CT/GA:	60	(complementary to (converted) bottom strand)
CT/GA/GA:	58	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	10466

Total methylated C's in CpG context:	37
Total methylated C's in CHG context:	28
Total methylated C's in CHH context:	143
Total methylated C's in Unknown context:	15

Total unmethylated C's in CpG context:	1699
Total unmethylated C's in CHG context:	1683
Total unmethylated C's in CHH context:	6876
Total unmethylated C's in Unknown context:	106

C methylated in CpG context:	2.1%
C methylated in CHG context:	1.6%
C methylated in CHH context:	2.0%
C methylated in unknown context (CN or CHN):	12.4%


Bismark completed in 0d 0h 0m 36s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-0.6/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99848 (99.85%) aligned concordantly 0 times
    29 (0.03%) aligned concordantly exactly 1 time
    123 (0.12%) aligned concordantly >1 times
0.15% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99838 (99.84%) aligned concordantly 0 times
    35 (0.04%) aligned concordantly exactly 1 time
    127 (0.13%) aligned concordantly >1 times
0.16% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99840 (99.84%) aligned concordantly 0 times
    34 (0.03%) aligned concordantly exactly 1 time
    126 (0.13%) aligned concordantly >1 times
0.16% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99842 (99.84%) aligned concordantly 0 times
    30 (0.03%) aligned concordantly exactly 1 time
    128 (0.13%) aligned concordantly >1 times
0.16% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	219
Mapping efficiency:	0.2%

Sequence pairs with no alignments under any condition:	99631
Sequence pairs did not map uniquely:	150
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	44	((converted) top strand)
GA/CT/CT:	62	(complementary to (converted) top strand)
GA/CT/GA:	54	(complementary to (converted) bottom strand)
CT/GA/GA:	59	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	9946

Total methylated C's in CpG context:	14
Total methylated C's in CHG context:	19
Total methylated C's in CHH context:	99
Total methylated C's in Unknown context:	9

Total unmethylated C's in CpG context:	1622
Total unmethylated C's in CHG context:	1700
Total unmethylated C's in CHH context:	6492
Total unmethylated C's in Unknown context:	85

C methylated in CpG context:	0.9%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	9.6%


Bismark completed in 0d 0h 0m 33s

====================
Bismark run complete
====================

/var/spool/slurm/d/job1154933/slurm_script: line 55: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	99	Cr_scaffold0000007_CT_converted	21820933	0	6M1I5M2I19M1I13M2D49M	=	21820930	-97	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-62	XN:i:0	XM:i:4	XO:i:4	XG:i:6	NM:i:10	MD:Z:0T1T4G35^GT19T29	YS:i:-73	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	147	Cr_scaffold0000007_CT_converted	21820930	0	4M2I5M1I5M2I19M1I13M2D44M	=	21820933	97	TATTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATT	FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-73	XN:i:0	XM:i:4	XO:i:5	XG:i:8	NM:i:12	MD:Z:1G3T4G35^GT19T24	YS:i:-62	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99707 (99.71%) aligned concordantly 0 times
    72 (0.07%) aligned concordantly exactly 1 time
    221 (0.22%) aligned concordantly >1 times
0.29% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99728 (99.73%) aligned concordantly 0 times
    50 (0.05%) aligned concordantly exactly 1 time
    222 (0.22%) aligned concordantly >1 times
0.27% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99766 (99.77%) aligned concordantly 0 times
    62 (0.06%) aligned concordantly exactly 1 time
    172 (0.17%) aligned concordantly >1 times
0.23% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99792 (99.79%) aligned concordantly 0 times
    37 (0.04%) aligned concordantly exactly 1 time
    171 (0.17%) aligned concordantly >1 times
0.21% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	388
Mapping efficiency:	0.4%

Sequence pairs with no alignments under any condition:	99422
Sequence pairs did not map uniquely:	190
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	117	((converted) top strand)
GA/CT/CT:	96	(complementary to (converted) top strand)
GA/CT/GA:	90	(complementary to (converted) bottom strand)
CT/GA/GA:	85	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	16134

Total methylated C's in CpG context:	66
Total methylated C's in CHG context:	57
Total methylated C's in CHH context:	397
Total methylated C's in Unknown context:	49

Total unmethylated C's in CpG context:	2573
Total unmethylated C's in CHG context:	2530
Total unmethylated C's in CHH context:	10511
Total unmethylated C's in Unknown context:	304

C methylated in CpG context:	2.5%
C methylated in CHG context:	2.2%
C methylated in CHH context:	3.6%
C methylated in unknown context (CN or CHN):	13.9%


Bismark completed in 0d 0h 0m 39s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99777 (99.78%) aligned concordantly 0 times
    43 (0.04%) aligned concordantly exactly 1 time
    180 (0.18%) aligned concordantly >1 times
0.22% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99764 (99.76%) aligned concordantly 0 times
    52 (0.05%) aligned concordantly exactly 1 time
    184 (0.18%) aligned concordantly >1 times
0.24% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99781 (99.78%) aligned concordantly 0 times
    40 (0.04%) aligned concordantly exactly 1 time
    179 (0.18%) aligned concordantly >1 times
0.22% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99773 (99.77%) aligned concordantly 0 times
    51 (0.05%) aligned concordantly exactly 1 time
    176 (0.18%) aligned concordantly >1 times
0.23% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	337
Mapping efficiency:	0.3%

Sequence pairs with no alignments under any condition:	99483
Sequence pairs did not map uniquely:	180
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	87	((converted) top strand)
GA/CT/CT:	92	(complementary to (converted) top strand)
GA/CT/GA:	74	(complementary to (converted) bottom strand)
CT/GA/GA:	84	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	14095

Total methylated C's in CpG context:	35
Total methylated C's in CHG context:	40
Total methylated C's in CHH context:	288
Total methylated C's in Unknown context:	27

Total unmethylated C's in CpG context:	2220
Total unmethylated C's in CHG context:	2358
Total unmethylated C's in CHH context:	9154
Total unmethylated C's in Unknown context:	249

C methylated in CpG context:	1.6%
C methylated in CHG context:	1.7%
C methylated in CHH context:	3.1%
C methylated in unknown context (CN or CHN):	9.8%


Bismark completed in 0d 0h 0m 36s

====================
Bismark run complete
====================

/var/spool/slurm/d/job1154933/slurm_script: line 71: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1_I60/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -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 Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	99	Cr_scaffold0000007_CT_converted	21820933	0	6M1I5M2I19M1I13M2D49M	=	21820930	-97	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-62	XN:i:0	XM:i:4	XO:i:4	XG:i:6	NM:i:10	MD:Z:0T1T4G35^GT19T29	YS:i:-73	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	147	Cr_scaffold0000007_CT_converted	21820930	0	4M2I5M1I5M2I19M1I13M2D44M	=	21820933	97	TATTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATT	FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-73	XN:i:0	XM:i:4	XO:i:5	XG:i:8	NM:i:12	MD:Z:1G3T4G35^GT19T24	YS:i:-62	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99773 (99.77%) aligned concordantly 0 times
    60 (0.06%) aligned concordantly exactly 1 time
    167 (0.17%) aligned concordantly >1 times
0.23% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99710 (99.71%) aligned concordantly 0 times
    72 (0.07%) aligned concordantly exactly 1 time
    218 (0.22%) aligned concordantly >1 times
0.29% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99798 (99.80%) aligned concordantly 0 times
    36 (0.04%) aligned concordantly exactly 1 time
    166 (0.17%) aligned concordantly >1 times
0.20% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99736 (99.74%) aligned concordantly 0 times
    46 (0.05%) aligned concordantly exactly 1 time
    218 (0.22%) aligned concordantly >1 times
0.26% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	379
Mapping efficiency:	0.4%

Sequence pairs with no alignments under any condition:	99434
Sequence pairs did not map uniquely:	187
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	117	((converted) top strand)
GA/CT/CT:	95	(complementary to (converted) top strand)
GA/CT/GA:	87	(complementary to (converted) bottom strand)
CT/GA/GA:	80	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	15882

Total methylated C's in CpG context:	65
Total methylated C's in CHG context:	55
Total methylated C's in CHH context:	310
Total methylated C's in Unknown context:	49

Total unmethylated C's in CpG context:	2533
Total unmethylated C's in CHG context:	2521
Total unmethylated C's in CHH context:	10398
Total unmethylated C's in Unknown context:	301

C methylated in CpG context:	2.5%
C methylated in CHG context:	2.1%
C methylated in CHH context:	2.9%
C methylated in unknown context (CN or CHN):	14.0%


Bismark completed in 0d 0h 0m 38s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1_I60/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-1 -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 Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99792 (99.79%) aligned concordantly 0 times
    38 (0.04%) aligned concordantly exactly 1 time
    170 (0.17%) aligned concordantly >1 times
0.21% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99789 (99.79%) aligned concordantly 0 times
    45 (0.04%) aligned concordantly exactly 1 time
    166 (0.17%) aligned concordantly >1 times
0.21% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99791 (99.79%) aligned concordantly 0 times
    47 (0.05%) aligned concordantly exactly 1 time
    162 (0.16%) aligned concordantly >1 times
0.21% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99781 (99.78%) aligned concordantly 0 times
    45 (0.04%) aligned concordantly exactly 1 time
    174 (0.17%) aligned concordantly >1 times
0.22% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	324
Mapping efficiency:	0.3%

Sequence pairs with no alignments under any condition:	99505
Sequence pairs did not map uniquely:	171
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	83	((converted) top strand)
GA/CT/CT:	84	(complementary to (converted) top strand)
GA/CT/GA:	75	(complementary to (converted) bottom strand)
CT/GA/GA:	82	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13828

Total methylated C's in CpG context:	33
Total methylated C's in CHG context:	40
Total methylated C's in CHH context:	309
Total methylated C's in Unknown context:	26

Total unmethylated C's in CpG context:	2167
Total unmethylated C's in CHG context:	2316
Total unmethylated C's in CHH context:	8963
Total unmethylated C's in Unknown context:	239

C methylated in CpG context:	1.5%
C methylated in CHG context:	1.7%
C methylated in CHH context:	3.3%
C methylated in unknown context (CN or CHN):	9.8%


Bismark completed in 0d 0h 0m 36s

====================
Bismark run complete
====================

/var/spool/slurm/d/job1154933/slurm_script: line 88: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1.2_I60/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ 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 Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.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:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	99	Cr_scaffold0000007_CT_converted	21820933	8	6M1I5M2I19M1I13M2D49M	=	21820930	-97	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-62	XN:i:0	XM:i:4	XO:i:4	XG:i:6	NM:i:10	MD:Z:0T1T4G35^GT19T29	YS:i:-73	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	147	Cr_scaffold0000007_CT_converted	21820930	8	4M2I5M1I5M2I19M1I13M2D44M	=	21820933	97	TATTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATT	FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-73	XN:i:0	XM:i:4	XO:i:5	XG:i:8	NM:i:12	MD:Z:1G3T4G35^GT19T24	YS:i:-62	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.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:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.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 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.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 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	77	*	0	0	*	*	0	0	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	141	*	0	0	*	*	0	0	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99645 (99.64%) aligned concordantly 0 times
    85 (0.09%) aligned concordantly exactly 1 time
    270 (0.27%) aligned concordantly >1 times
0.35% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99741 (99.74%) aligned concordantly 0 times
    59 (0.06%) aligned concordantly exactly 1 time
    200 (0.20%) aligned concordantly >1 times
0.26% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99674 (99.67%) aligned concordantly 0 times
    58 (0.06%) aligned concordantly exactly 1 time
    268 (0.27%) aligned concordantly >1 times
0.33% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99706 (99.71%) aligned concordantly 0 times
    89 (0.09%) aligned concordantly exactly 1 time
    205 (0.20%) aligned concordantly >1 times
0.29% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	524
Mapping efficiency:	0.5%

Sequence pairs with no alignments under any condition:	99269
Sequence pairs did not map uniquely:	207
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	155	((converted) top strand)
GA/CT/CT:	136	(complementary to (converted) top strand)
GA/CT/GA:	118	(complementary to (converted) bottom strand)
CT/GA/GA:	115	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	20258

Total methylated C's in CpG context:	104
Total methylated C's in CHG context:	90
Total methylated C's in CHH context:	761
Total methylated C's in Unknown context:	91

Total unmethylated C's in CpG context:	3182
Total unmethylated C's in CHG context:	3097
Total unmethylated C's in CHH context:	13024
Total unmethylated C's in Unknown context:	488

C methylated in CpG context:	3.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	5.5%
C methylated in unknown context (CN or CHN):	15.7%


Bismark completed in 0d 0h 0m 40s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-1.2_I60/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ 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 Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.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:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.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:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	99	Cr_scaffold0000014_GA_converted	14427642	0	7M5I22M3D6M1I20M	=	14427637	-63	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	AS:i:-60	XN:i:0	XM:i:3	XO:i:3	XG:i:9	NM:i:12	MD:Z:2C26^AAA6T10C8	YS:i:-66	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	147	Cr_scaffold0000014_GA_converted	14427637	0	12M5I22M3D6M1I15M	=	14427642	63	AACTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATA	FFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-66	XN:i:0	XM:i:4	XO:i:3	XG:i:9	NM:i:13	MD:Z:0T6C26^AAA6T10C3	YS:i:-60	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.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 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	83	Cr_scaffold0000006_CT_converted	4815191	2	16M2D26M2I2M1I6M1D8M	=	4815196	65	TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATT	FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-68	XS:i:-72	XN:i:0	XM:i:5	XO:i:4	XG:i:6	NM:i:11	MD:Z:2G0A8A3^AA0G33^A4G3	YS:i:-70	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	163	Cr_scaffold0000006_CT_converted	4815196	2	11M2D26M2I2M1I6M1D6M1I6M	=	4815191	-65	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	AS:i:-70	XS:i:-72	XN:i:0	XM:i:4	XO:i:5	XG:i:7	NM:i:11	MD:Z:7A3^AA0G33^A4G4A2	YS:i:-68	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.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 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99723 (99.72%) aligned concordantly 0 times
    60 (0.06%) aligned concordantly exactly 1 time
    217 (0.22%) aligned concordantly >1 times
0.28% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99708 (99.71%) aligned concordantly 0 times
    58 (0.06%) aligned concordantly exactly 1 time
    234 (0.23%) aligned concordantly >1 times
0.29% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99728 (99.73%) aligned concordantly 0 times
    54 (0.05%) aligned concordantly exactly 1 time
    218 (0.22%) aligned concordantly >1 times
0.27% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    99700 (99.70%) aligned concordantly 0 times
    69 (0.07%) aligned concordantly exactly 1 time
    231 (0.23%) aligned concordantly >1 times
0.30% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	476
Mapping efficiency:	0.5%

Sequence pairs with no alignments under any condition:	99330
Sequence pairs did not map uniquely:	194
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	110	((converted) top strand)
GA/CT/CT:	135	(complementary to (converted) top strand)
GA/CT/GA:	121	(complementary to (converted) bottom strand)
CT/GA/GA:	110	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	18605

Total methylated C's in CpG context:	77
Total methylated C's in CHG context:	66
Total methylated C's in CHH context:	843
Total methylated C's in Unknown context:	78

Total unmethylated C's in CpG context:	2851
Total unmethylated C's in CHG context:	2934
Total unmethylated C's in CHH context:	11834
Total unmethylated C's in Unknown context:	457

C methylated in CpG context:	2.6%
C methylated in CHG context:	2.2%
C methylated in CHH context:	6.6%
C methylated in unknown context (CN or CHN):	14.6%


Bismark completed in 0d 0h 0m 37s

====================
Bismark run complete
====================

/var/spool/slurm/d/job1154933/slurm_script: line 104: 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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-2/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	99	Cr_scaffold0000007_CT_converted	21820933	0	6M1I5M2I19M1I13M2D49M	=	21820930	-97	ATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATTTTGTT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-62	XN:i:0	XM:i:4	XO:i:4	XG:i:6	NM:i:10	MD:Z:0T1T4G35^GT19T29	YS:i:-73	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	147	Cr_scaffold0000007_CT_converted	21820930	0	4M2I5M1I5M2I19M1I13M2D44M	=	21820933	97	TATTAATATTATAAAAATTTTTTATTGTATAGTTAAAGTTTTTGTAATATTGGTGAGGGTAGTTTTTGATAATAAATTTATTTATAGGTTATTATT	FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-73	XS:i:-187	XN:i:0	XM:i:4	XO:i:5	XG:i:8	NM:i:12	MD:Z:1G3T4G35^GT19T24	YS:i:-62	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	99	Cr_scaffold0000001_GA_converted	11377254	2	22M3I4M4I4M2D5M1I6M7I6M4I2M1I18M1D9M	=	11377249	-84	ATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATTTTATT	FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-145	XS:i:-169	XN:i:0	XM:i:6	XO:i:8	XG:i:23	NM:i:29	MD:Z:30^CA9C17A2T1T0C3^A8A0	YS:i:-156	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	147	Cr_scaffold0000001_GA_converted	11377249	2	27M3I4M4I4M2D5M1I6M7I6M4I2M1I8M4I6M1D4M	=	11377254	84	CACCAATATTACAAAAACTTTTTATTATATAATTAAAATTTTTATAATATTAATAAAAATAATTTTTAATAATAAATTTATTTATAAATTATTATT	FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-156	XS:i:-171	XN:i:0	XM:i:5	XO:i:9	XG:i:27	NM:i:32	MD:Z:1T0A0A31^CA9C23^C3A0	YS:i:-145	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	83	Cr_scaffold0000008_CT_converted	19441986	0	3M2I8M2I39M4I13M1I4M10I3M1I6M	=	19441989	82	AATAAAATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	AS:i:-126	XN:i:0	XM:i:6	XO:i:6	XG:i:20	NM:i:26	MD:Z:7T3A25T8T12T12T3	YS:i:-130	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	163	Cr_scaffold0000008_CT_converted	19441989	0	8M2I39M4I13M1I4M9I9M1I6M	=	19441986	-82	AATAATAATTTATAAATAAATTTATTATTAAAAATTATTTTTATTAATATTATAAAAATTTTAATTATATAATAAAAAGTTTTTGTAATATTGGTG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	AS:i:-130	XS:i:-177	XN:i:0	XM:i:9	XO:i:5	XG:i:17	NM:i:26	MD:Z:4T3A25T8T12T11A1T4A0T2	YS:i:-126	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1316:1016/1	83	Cr_scaffold0000011_GA_converted	10413175	2	28M1I3M18I4M1I6M1D13M1I6M1D15M	=	10413180	77	AACAAAATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	AS:i:-153	XS:i:-153	XN:i:0	XM:i:9	XO:i:6	XG:i:23	NM:i:32	MD:Z:0T1T38^T2A0A3T1A3T5^T8T0A5	YS:i:-157	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1316:1016/2	163	Cr_scaffold0000011_GA_converted	10413180	2	23M1I3M18I4M1I6M1D13M1I6M1D8M4I2M2I4M	=	10413175	-77	AATAATAACCTATAAATAAATTTATTATCAAAAACTACCCTCACCAATATTACAAAAACTTTAACTATACAATAAAAAATTTTTATAATATTAATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFF	AS:i:-157	XS:i:-159	XN:i:0	XM:i:5	XO:i:8	XG:i:29	NM:i:34	MD:Z:36^T2A0A3T1A3T5^T14	YS:i:-153	YT:Z:CP

>>> Writing bisulfite mapping results to Sealice_F1_S20_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz
100000 reads; of these:
  100000 (100000 reads; of these:
100.00  %100000) were paired; of these: (
    13390 (13.39100.00%%) aligned concordantly 0 times) were paired; of these:

        384414509 ( (3.8414.51%%) aligned concordantly exactly 1 time) aligned concordantly 0 times

        827664500 ( (82.774.50%%) aligned concordantly >1 times) aligned concordantly exactly 1 time

86.61    %80991 overall alignment rate (
80.99%) aligned concordantly >1 times
85.49% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    14376 (14.38%) aligned concordantly 0 times
    4523 (4.52%) aligned concordantly exactly 1 time
    81101 (81.10%) aligned concordantly >1 times
85.62% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    13336 (13.34%) aligned concordantly 0 times
    3812 (3.81%) aligned concordantly exactly 1 time
    82852 (82.85%) aligned concordantly >1 times
86.66% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	89667
Mapping efficiency:	89.7%

Sequence pairs with no alignments under any condition:	251
Sequence pairs did not map uniquely:	10082
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	23234	((converted) top strand)
GA/CT/CT:	21132	(complementary to (converted) top strand)
GA/CT/GA:	21445	(complementary to (converted) bottom strand)
CT/GA/GA:	23856	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2833737

Total methylated C's in CpG context:	29714
Total methylated C's in CHG context:	29408
Total methylated C's in CHH context:	384942
Total methylated C's in Unknown context:	74898

Total unmethylated C's in CpG context:	308568
Total unmethylated C's in CHG context:	312815
Total unmethylated C's in CHH context:	1768290
Total unmethylated C's in Unknown context:	231248

C methylated in CpG context:	8.8%
C methylated in CHG context:	8.6%
C methylated in CHH context:	17.9%
C methylated in unknown context (CN or CHN):	24.5%


Bismark completed in 0d 0h 2m 16s

====================
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/strigg/data/Caligus/GENOMES/	(absolute path is '/gscratch/srlab/strigg/data/Caligus/GENOMES/)'
FastQ format assumed (by default)
Processing sequences up to read no. 100000 from the input file
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20190806_100K_Calig'):
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
/gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig/AS-2/
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/strigg/analyses/20190806_100K_Calig

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/strigg/data/Caligus/GENOMES/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 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/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
Writing a C -> T converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz to Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz (100001 sequences in total)

Input files are Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	99	Cr_scaffold0000014_GA_converted	14427642	2	7M5I22M3D6M1I20M	=	14427637	-63	AATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATAAAAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	AS:i:-60	XS:i:-67	XN:i:0	XM:i:3	XO:i:3	XG:i:9	NM:i:12	MD:Z:2C26^AAA6T10C8	YS:i:-66	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	147	Cr_scaffold0000014_GA_converted	14427637	2	12M5I22M3D6M1I15M	=	14427642	63	AACTAAATTATATATATTAATAATTAATAAAATAATAATTAAATTAAAAAAAAAAAAAATA	FFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-66	XS:i:-64	XN:i:0	XM:i:4	XO:i:3	XG:i:9	NM:i:13	MD:Z:0T6C26^AAA6T10C3	YS:i:-60	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	83	Cr_scaffold0000004_CT_converted	20430829	0	37M2I4M4I14M	=	20430834	61	TTTTTTATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATT	FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-58	XS:i:-72	XN:i:0	XM:i:5	XO:i:2	XG:i:6	NM:i:11	MD:Z:0A1A46T1G2A0	YS:i:-54	YT:Z:CP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	163	Cr_scaffold0000004_CT_converted	20430834	0	32M2I4M4I13M1D6M	=	20430829	-61	TATTTTTTTTTTTTTTAATTTAATTATTATTTTATTAATTATTAATATATATAATTTAGTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	AS:i:-54	XS:i:-72	XN:i:0	XM:i:3	XO:i:3	XG:i:7	NM:i:10	MD:Z:44T1G2^A5A0	YS:i:-58	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A00177:85:HCW7VDRXX:1:2101:1407:1016/1	77	*	0	0	*	*	0	0	AATTATGTATGTTAATAGTTAATGGAGTAATAATTAAGTTAGAGAGGAGGAGAATAAGAAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF	YT:Z:UP
A00177:85:HCW7VDRXX:1:2101:1407:1016/2	141	*	0	0	*	*	0	0	TATTCTCCTCCTCTCTAACTTAATTATTACTCCATTAACTATTAACATACATAATTCAATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFF	YT:Z:UP

>>> Writing bisulfite mapping results to Sealice_F2_S22_R1_001_trimmed.5bp_3prime_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz and /gscratch/scrubbed/strigg/TRIM_cat/Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz
100000100000 reads; of these: reads; of these:

    100000100000 ( (100.00100.00%%) were paired; of these:) were paired; of these:

        1939619397 ( (19.4019.40%%) aligned concordantly 0 times) aligned concordantly 0 times

        41344144 ( (4.134.14%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time

        7647076459 ( (76.4776.46%%) aligned concordantly >1 times) aligned concordantly >1 times

80.6080.60%% overall alignment rate overall alignment rate

100000 reads; of these:
  100000 (100.00%) were paired; of these:
    21707 (21.71%) aligned concordantly 0 times
    4405 (4.41%) aligned concordantly exactly 1 time
    73888 (73.89%) aligned concordantly >1 times
78.29% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    21576 (21.58%) aligned concordantly 0 times
    4481 (4.48%) aligned concordantly exactly 1 time
    73943 (73.94%) aligned concordantly >1 times
78.42% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq, Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq, Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq and Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Number of paired-end alignments with a unique best hit:	90213
Mapping efficiency:	90.2%

Sequence pairs with no alignments under any condition:	755
Sequence pairs did not map uniquely:	9032
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	23221	((converted) top strand)
GA/CT/CT:	21944	(complementary to (converted) top strand)
GA/CT/GA:	22157	(complementary to (converted) bottom strand)
CT/GA/GA:	22891	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2681591

Total methylated C's in CpG context:	31095
Total methylated C's in CHG context:	30686
Total methylated C's in CHH context:	454686
Total methylated C's in Unknown context:	91282

Total unmethylated C's in CpG context:	277535
Total unmethylated C's in CHG context:	278006
Total unmethylated C's in CHH context:	1609583
Total unmethylated C's in Unknown context:	233661

C methylated in CpG context:	10.1%
C methylated in CHG context:	9.9%
C methylated in CHH context:	22.0%
C methylated in unknown context (CN or CHN):	28.1%


Bismark completed in 0d 0h 2m 8s

====================
Bismark run complete
====================

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