Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.5.1-linux-x86_64/bowtie2 --version' [2.3.5])
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/Pgenr/OFS/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/OFS/)'
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200316/TG_EPI-Test3'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/20bp_clip/EPI-167_S10_L002_R1_001_val_1.20bp-trim.fq.gz
/gscratch/srlab/strigg/data/Pgenr/FASTQS/20bp_clip/EPI-167_S10_L002_R2_001_val_2.20bp-trim.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Unable to create directory /gscratch/scrubbed/strigg/analyses/20200317/TG_EPI-Test3/ No such file or directory
Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.5.1-linux-x86_64/bowtie2 --version' [2.3.5])
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/Pgenr/OFS/	(absolute path is '/gscratch/srlab/strigg/data/Pgenr/OFS/)'
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/scrubbed/strigg/analyses/20200316/TG_EPI-Test3'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Unable to create directory /gscratch/scrubbed/strigg/analyses/20200317/TG_EPI-Test3/ No such file or directory

 *** Bismark methylation extractor version v0.19.0 ***

Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark paired-end SAM format specified (default)
Number of cores to be used: 14
Output will be written to the current directory ('/gscratch/scrubbed/strigg/analyses/20200316/TG_EPI-Test3')


Summarising bedGraph parameters:
===============================================================
Generating additional output in bedGraph and coverage format
bedGraph format:	<Chromosome> <Start Position> <End Position> <Methylation Percentage>
coverage format:	<Chromosome> <Start Position> <End Position> <Methylation Percentage> <count methylated> <count non-methylated>

Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>*.bam<< for signs of file truncation...
Captured error message: '[E::hts_open_format] Failed to open file *.bam'

[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...