I have beein trying to feed an sra accession to partie. Those attempts always fail for me, including the tests at https://github.com/linsalrob/partie/blob/master/TEST.md
The underlying issue seems to be that fastq-dump (at least in the versions i have tried out) expects an argument specifying line width after --fasta
Changing line 162 in the partie perl script to specify default as the line width has fixed this issue for me when using fastq-dump 2.11.0
The "Running Partie" section here on github also mentions the option of providing a .txt file with IDs, but i did not manage to get that working. Does this functionality just not exist in the current relase?
Thank your for the great tool, it is very useful to me!
I have beein trying to feed an sra accession to partie. Those attempts always fail for me, including the tests at https://github.com/linsalrob/partie/blob/master/TEST.md
The underlying issue seems to be that fastq-dump (at least in the versions i have tried out) expects an argument specifying line width after
--fastaChanging line 162 in the partie perl script to specify
defaultas the line width has fixed this issue for me when using fastq-dump 2.11.0The "Running Partie" section here on github also mentions the option of providing a .txt file with IDs, but i did not manage to get that working. Does this functionality just not exist in the current relase?
Thank your for the great tool, it is very useful to me!