After running countKmers, I found that the file sorted_files.txt had incorrect specification of the sample folders.
The sample folders were indicated as Reads_catrim.Hcor_SM05L02_Red.fastq.gz, etc.
The sorted_files.txt included lines like so
/Hcor/Reads_Reads_catrim.Hcor_SM05L02_Red.fastq.gz/Reads_catrim.Hcor_SM05L02Red.fastq.gz
Obviously, an extra Reads was appended to the folder specification.
I changed this to a single "Reads_" with
sed -i.bak 's/ReadsReads/Reads_/' sorted_files.txt
But would be good to change in code.
atifrahman
commented
5 years ago
After running countKmers, I found that the file sorted_files.txt had incorrect specification of the sample folders. The sample folders were indicated as Reads_catrim.Hcor_SM05L02_Red.fastq.gz, etc. The sorted_files.txt included lines like so /Hcor/Reads_Reads_catrim.Hcor_SM05L02_Red.fastq.gz/Reads_catrim.Hcor_SM05L02Red.fastq.gz Obviously, an extra Reads was appended to the folder specification. I changed this to a single "Reads_" with sed -i.bak 's/ReadsReads/Reads_/' sorted_files.txt But would be good to change in code.