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/froger/Mcap_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Mcap_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth13_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth13_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Mcap_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Mcap_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth14_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth14_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Mcap_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Mcap_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth15_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth15_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Mcap_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Mcap_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth4_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth4_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Mcap_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Mcap_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth5_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth5_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Pact_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Pact_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth13_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth13_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Pact_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Pact_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth14_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth14_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Pact_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Pact_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth15_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth15_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Pact_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Pact_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth4_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth4_R2_001_val_1.fq.gz' does not exist, please respecify! 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/froger/Pact_Genome/ (absolute path is '/gscratch/srlab/sr320/data/froger/Pact_Genome/)' FastQ format assumed (by default) Processing sequences up to read no. 10000000 from the input file 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/sr320/030520-fr01'): /gscratch/scrubbed/strigg/analyses/20200306/Meth5_R1_001_val_1.fq.gz Supplied filename '/gscratch/scrubbed/strigg/analyses/20200306/Meth5_R2_001_val_1.fq.gz' does not exist, please respecify!