I tested the version with no "number" parameter of PMDtools and it worked fine.
I corrected the log file path of Bowtie2_Index and Samtools_Faidx which were giving warnings previously in issue #85.
Add some information on ways to download the databases in the README.
Make "ancient" the input file of Bowtie2_Index and Samtools_Faidx because the full database can be downloaded and rerunning the database building and indexing is too much time and memory intensive.
I tested the version with no "number" parameter of PMDtools and it worked fine. I corrected the log file path of Bowtie2_Index and Samtools_Faidx which were giving warnings previously in issue #85. Add some information on ways to download the databases in the README. Make "ancient" the input file of Bowtie2_Index and Samtools_Faidx because the full database can be downloaded and rerunning the database building and indexing is too much time and memory intensive.