Empty summary.tsv file

[pneumowidow]

Hi,

I downloaded seroba via conda and ran it as recommended. However, although I get pred.tsv output for all genomes, I don't get a summary.tsv output. I used a for loop to run the commands for all my genome files since it was easier that way (see below):

#define serotype
for f in ./*_1P.fastq
do
 base=$(basename $f "_1P.fastq")
 basebam=$(basename $f "_L1_out_1P.fastq")
 seroba runSerotyping $out/Pneumocat-dir/ ${base}_1P.fastq ${base}_2P.fastq $out/summary_out/seroBA_${basebam} &&
 seroba summary $out/summary_out/seroBA_${basebam}
done

When I realized that I didn't get the summary output file, I decided to run the seroba summary command for just one output folder (instead of the for loop), but that still didn't work. As you can see in the snapshot below, the size of the file remains 0 KB.

Is there something I did wrong? Thanks for your help in advance.

[eppinglen]

Hi @pneumowidow,

the "summary" function can not directly be used on the output folder of a single run. Instead you can use: seroba summary $out/summary_out/ after your for loop is done.

[pneumowidow]

Ahh...ok. makes sense. Thank you!