Bowtie 2 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-1.4/bin/samtools'
Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/	(absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)'
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary!
Paired-end mapping requires the format: -1 <mates1> -2 <mates2>, please respecify!
xargs: /gscratch/srlab/programs/Bismark-0.22.3/bismark: exited with status 255; aborting
/var/spool/slurm/d/job1966545/slurm_script: line 48: -2: command not found
find: ‘*.bam’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.

 *** Bismark methylation extractor version v0.22.3 ***

Trying to determine the type of mapping from the SAM header line of file *deduplicated.bam

[FATAL ERROR]:	File >>*deduplicated.bam<< did not exist. Please re-specify file names and try again...

Found no potential alignment reports in the current directory. Please specify a single Bismark alignment report file using the option '--alignment_report FILE'


  SYNOPSIS:

  This script uses a Bismark alignment report to generate a graphical HTML report page. Optionally, further reports of
  the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. If several
  Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename
  will be derived from the Bismark alignment report file. bismark2report attempts to find optional reports automatically based
  on the file basename.


  USAGE: bismark2report [options]


-o/--output <filename>     Name of the output file (optional). If not specified explicitly, the output filename will be derived
                           from the Bismark alignment report file. Specifying an output filename only works if the HTML report is
                           to be generated for a single Bismark alignment report (and potentially additional reports).

--dir                      Output directory. Output is written to the current directory if not specified explicitly.


--alignment_report FILE    If not specified explicitly, bismark2report attempts to find Bismark report file(s) in the current
                           directory and produces a separate HTML report for each mapping report file. Based on the basename of
                           the Bismark mapping report, bismark2report will also attempt to find the other Bismark reports (see below)
                           for inclusion into the HTML report. Specifying a Bismark alignment report file is mandatory.

--dedup_report FILE        If not specified explicitly, bismark2report attempts to find a deduplication report file with the same
                           basename as the Bismark mapping report (generated by deduplicate_bismark) in the
                           current working directory. Including a deduplication report is optional, and using the FILE 'none'
                           will skip this step entirely.

--splitting_report FILE    If not specified explicitly, bismark2report attempts to find a splitting report file with the same
                           basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current
                           working directory. Including a splitting report is optional, and using the FILE 'none' will skip this
                           step entirely.

--mbias_report FILE        If not specified explicitly, bismark2report attempts to find a single M-bias report file with the same
                           basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current
                           working directory. Including an M-Bias report is optional, and using the FILE 'none' will skip this step
                           entirely.

--nucleotide_report FILE   If not specified explicitly, bismark2report attempts to find a single nucleotide coverage report file
                           with the same basename as the Bismark mapping report (generated by Bismark with the option
                           '--nucleotide_coverage') in the current working directory. Including a nucleotide coverage statistics
                           report is optional, and using the FILE 'none' will skip this report entirely.

                           Script last modified: 03 May 2019

No Bismark/Bowtie2 single-end BAM files detected
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/HISAT2 single-end BAM files detected
No Bismark/HISAT2 paired-end BAM files detected

Error: No Bismark BAM files found to generate a Bismark project summary. Please respecify...

USAGE:
bismark2summary (*.bam), or bismark2summary --help for more information at /gscratch/srlab/programs/Bismark-0.22.3/bismark2summary line 201.
[INFO   ]         multiqc : This is MultiQC v1.8
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /gscratch/scrubbed/sr320/060821-big
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete
find: ‘*deduplicated.bam’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.
find: ‘*.sorted.bam’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.
find: ‘*deduplicated.bismark.cov.gz’: No such file or directory
basename: missing operand
Try 'basename --help' for more information.
cat: *merged_CpG_evidence.cov: No such file or directory
cat: *merged_CpG_evidence.cov: No such file or directory
cat: *merged_CpG_evidence.cov: No such file or directory
cat: *merged_CpG_evidence.cov: No such file or directory