Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.4.1-linux-x86_64/bowtie2 --version' [2.4.1]) 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/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ (absolute path is '/gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/)' Failed to move to directory /gscratch/scrubbed/yaaminiv/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/Bisulfite_Genome/CT_conversion/: No such file or directory