Hi, I have run BS-SNPer on my bismark alignments and it seems to have run properly (I get SNP output files), however, in the error file I get several errors pasted below:
SNP process ends...
SNP process completed.
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 1: 00: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 2: .SH: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 3: .PP: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 4: syntax error near unexpected token (' /lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 4: samtools - Utilities for the Sequence Alignment/Map (SAM) format'
Does anyone know what this is about and if it is an issue? I am just wondering if my SNP files are fine.
Hi, I have run BS-SNPer on my bismark alignments and it seems to have run properly (I get SNP output files), however, in the error file I get several errors pasted below:
SNP process ends...
SNP process completed.
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 1: 00: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 2: .SH: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 3: .PP: command not found
/lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 4: syntax error near unexpected token
(' /lustre04/scratch/janayfox/guppyWGBS/BS-SNPer/BS-Snper-master/samtools-0.1.19/samtools: line 4:samtools - Utilities for the Sequence Alignment/Map (SAM) format'Does anyone know what this is about and if it is an issue? I am just wondering if my SNP files are fine.