ampliconsorter frozen

[capoony]

Hi Andy,

I am facing a rather curious problem. When starting ampliconsorter with an admittedly small dataset (no more reads available), ampliconsorter freezes and never stops running. I have used the following settings:

./ampliconsorter.py  \
   -i AATS.fastq  \
   -np 1 \
   -maxr 500 \
   -o output/

I have attached the AATS.fastq (gzipped) for reproduciblity.

Thanks, Martin AATS.fastq.gz

[avierstr]

Hi Martin,

I'm having the same result with your file. When printing the readlengths, it seems that they are to different in length (max 1.05 difference allowed to compare them with each other). So nothing has to be done according to the script but that exceptional occurrence is not catched in an exit of the program. I will update it so it exits when this happens.

Best regards, Andy

python3 amplicon_sorter.py -i AATS.fastq -np 1 -maxr 500 -o output
Reading AATS.fastq
1261
427
333
303
877
700
753
AATS.fastq contains 7 reads.
--> Low number of reads, reading all 7 out of 7 sequences longer than 300bp

[capoony]

Hi Andy, wow!! Thanks for your light-speed response and for looking into this! I was suspecting something like this.

best regards,

Martin

[capoony]

Hi Andy, sorry for being a pain, but when do you expect a fix? Alternatively, we could also have a try and commit on a different branch. many thanks! :-)

Best, Martin

[avierstr]

Hi Martin, I did not look into that because I did not know it was urgent. It was only a small fix. Here is the updated file. I will upload it to the main branch one of the next days. Best regards, Andy amplicon_sorter_2024_02_20.py.zip

[capoony]

Dear Andy,

oh my, sorry! Hope I did not stress you! Thanks a lot, I'll test the new versions asap.

Many greetings,

Martin

[capoony]

Thanks Andy, works like a charm!

Many greetings,

Martin