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 found here: '/gscratch/srlab/programs/samtools-1.9/samtools'
Reference genome folder provided is /gscratch/srlab/sam/data/C_gigas/genomes/	(absolute path is '/gscratch/srlab/sam/data/C_gigas/genomes/)'
Processing sequences up to read no. 100000 from the input file
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4

Input files to be analysed (in current folder '/gscratch/scrubbed/samwhite/outputs/20190222_cgigas_pe_bismark/subset_100000'):
/gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz
/gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Setting parallelization to single-threaded (default)

Current working directory is: /gscratch/scrubbed/samwhite/outputs/20190222_cgigas_pe_bismark/subset_100000

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_gigas/genomes/

Single-core mode: setting pid to 1

Paired-end alignments will be performed
=======================================

The provided filenames for paired-end alignments are /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz
Input files are in FastQ format
Processing reads up to sequence no. 100000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz
Writing a C -> T converted version of the input file cgig_bsseq_pe_all_R1.fastq.gz to cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file cgig_bsseq_pe_all_R1.fastq.gz (100001 sequences in total)

Processing reads up to sequence no. 100000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz
Writing a G -> A converted version of the input file cgig_bsseq_pe_all_R2.fastq.gz to cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file cgig_bsseq_pe_all_R2.fastq.gz (100001 sequences in total)

Input files are cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq (FastQ)
Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_gigas/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500

Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1	99	scaffold750_CT_converted	577176	1	36M	=	577200	60	AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG	CC@FDFFFHHGHHJFBGIIJJIJEHGIJIJJJJJJG	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:36	YS:i:0	YT:Z:CP
HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2	147	scaffold750_CT_converted	577200	1	36M	=	577176	-60	AGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAG	GJJJIJJJJJJJJJJJJJJJJJJHHHHHD;FFFCC@	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:36	YS:i:0	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1	83	scaffold393_GA_converted	143720	1	36M	=	143706	-50	CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT	GJJJJJJIJIGHEJIJJIIGBFJHHGHHFFFDF@CC	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:36	YS:i:0	YT:Z:CP
HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2	163	scaffold393_GA_converted	143706	1	36M	=	143720	50	CTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCT	@CCFFF;DHHHHHJJJJJJJJJJJJJJJJJJIJJJG	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:36	YS:i:0	YT:Z:CP

>>> Writing bisulfite mapping results to cgig_bsseq_pe_all_R1_bismark_bt2_pe.bam <<<


Reading in the sequence files /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz
Chromosomal sequence could not be extracted for	HWI-ST700693:385:C3ATLACXX:4:1101:5142:25699	C24196	1
Chromosomal sequence could not be extracted for	HWI-ST700693:385:C3ATLACXX:4:1105:4856:63835	C22548	1
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    81250 (81.25%) aligned concordantly 0 times
    9409 (9.41%) aligned concordantly exactly 1 time
    9341 (9.34%) aligned concordantly >1 times
18.75% overall alignment rate
100000 reads; of these:
  100000 (100.00%) were paired; of these:
    81450 (81.45%) aligned concordantly 0 times
    9224 (9.22%) aligned concordantly exactly 1 time
    9326 (9.33%) aligned concordantly >1 times
18.55% overall alignment rate
Processed 100000 sequences in total


Successfully deleted the temporary files cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	100000
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	216463

Total methylated C's in CpG context:	3093
Total methylated C's in CHG context:	41
Total methylated C's in CHH context:	156
Total methylated C's in Unknown context:	1

Total unmethylated C's in CpG context:	23065
Total unmethylated C's in CHG context:	35983
Total unmethylated C's in CHH context:	154125
Total unmethylated C's in Unknown context:	206

C methylated in CpG context:	11.8%
C methylated in CHG context:	0.1%
C methylated in CHH context:	0.1%
C methylated in unknown context (CN or CHN):	0.5%


Bismark completed in 0d 0h 0m 40s

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