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/v074/	(absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)'
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/sr320/0821-ba'):
/gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz
/gscratch/scrubbed/sr320/0821/Pg_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/sr320/0821-ba

Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp)

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz and /gscratch/scrubbed/sr320/0821/Pg_val_2.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file Pg_val_1.fq.gz to Pg_val_1.fq.gz_C_to_T.fastq
slurmstepd: error: *** JOB 1207492 ON n2441 CANCELLED AT 2019-08-21T12:45:38 ***