I have used this script to successfully create mapped reads with my dataset. I have since added more samples to my dataset and now this script isn't working for me at all, not even on the samples that it previously worked for. The log file shows this for every single sample
"Generating on-target reads for files for sample name
Keeping all reads for sample name"
But the mapped .fasta file will be empty for nearly all the samples, and the ones that have reads in them only have a dozen or so bases. The samples that were previously run had anywhere from 500MB to 4GB in size. And when I compare the files within the 01_data directory, the new consensus files are exactly the same as the old consensus files, so it is definitely something going wrong with the mapping script. Are there any packages that bash might not be finding?"
The command I am running is simply
bash 2_extract_mapped_reads.sh -b ./01_data/ -o ./mapped_reads
I have used this script to successfully create mapped reads with my dataset. I have since added more samples to my dataset and now this script isn't working for me at all, not even on the samples that it previously worked for. The log file shows this for every single sample
"Generating on-target reads for files for sample name Keeping all reads for sample name"
But the mapped .fasta file will be empty for nearly all the samples, and the ones that have reads in them only have a dozen or so bases. The samples that were previously run had anywhere from 500MB to 4GB in size. And when I compare the files within the 01_data directory, the new consensus files are exactly the same as the old consensus files, so it is definitely something going wrong with the mapping script. Are there any packages that bash might not be finding?"
The command I am running is simply
bash 2_extract_mapped_reads.sh -b ./01_data/ -o ./mapped_readsThanks, Steve