Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893.
Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0])
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/geoduck/v01/	(absolute path is '/gscratch/srlab/sr320/data/geoduck/v01/)'
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!

Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1218'):
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz
/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_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!)
Setting parallelization to single-threaded (default)

Summary of all aligner options:	-q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /gscratch/scrubbed/sr320/1218

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/

chr Scaffold_01 (89643857 bp)
chr Scaffold_02 (69596280 bp)
chr Scaffold_03 (57743597 bp)
chr Scaffold_04 (65288255 bp)
chr Scaffold_05 (67248332 bp)
chr Scaffold_06 (61759565 bp)
chr Scaffold_07 (43120122 bp)
chr Scaffold_08 (61151155 bp)
chr Scaffold_09 (38581958 bp)
chr Scaffold_10 (53961475 bp)
chr Scaffold_11 (51449921 bp)
chr Scaffold_12 (50438331 bp)
chr Scaffold_13 (44396874 bp)
chr Scaffold_14 (45393038 bp)
chr Scaffold_15 (47938513 bp)
chr Scaffold_16 (31980953 bp)
chr Scaffold_17 (34923512 bp)
chr Scaffold_18 (27737463 bp)

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-103_S27_L005_R2_001_val_2.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EPI-103_S27_L005_R1_001_val_1.fq.gz to EPI-103_S27_L005_R1_001_val_1.fq.gz_C_to_T.fastq
slurmstepd: error: *** JOB 1578809 ON n2226 CANCELLED AT 2019-12-18T10:16:24 ***