TideHunter with flags doesn't output different data format or filter data

[mcrone]

Hi

Thanks for creating TideHunter, it is exactly what I need for a specific application that I'm working on. I've tried running the tool, but adding in the -m, -f, -l flags doesn't seem to make a difference to the final data output (-c does). I am not able to get anything other than a fasta output and I can't filter on the minimum length of the output.

I've tried using both the direct command line and the docker container.

This is my command: ./bin/TideHunter -u -l -m 1000 -c 2 -f 2 ./fastq/barcode43.fastq.gz > outputtest.out

This is the docker command: docker run -v "/Users/xxxxx/xxxxx/xxxxx/barcode43":/data quay.io/biocontainers/tidehunter:1.5.4--h43eeafb_2 TideHunter -u -l -m 1000 -c 3 -f 2 /data/barcode43.fastq.gz -o data/outputtest.out

Is there anything obvious that I am doing incorrectly?

[yangao07]

"-f 2" should give you the tabular output, not fasta output.
Can you paste some of the output results you have here?

[mcrone]

This works with the normal source on the repository. I've found that the docker version does not work (even when building the image from scratch).

When running the following command:
docker run -v "/Users/xxxxxx/barcode43":/data quay.io/biocontainers/tidehunter:1.5.4--h43eeafb_2 TideHunter -u -f 2 /data/barcode43.fastq.gz --output data/outputtest.out

Docker doesn't seem to accept the use of '>'.

Either way, I end up with the following output:
f3145286-baa6-4e70-89ad-44d859164aa2 rep0 sub0 AGTCAACAACACCGCCAGCAGGCCGCGCACAATGCGCCCTTCGCTGTCGCCAAAGAAATGCATTTTGCCGTTTTCAGCCACTGTATATCCCAGCCAGACGCGGTTTTCGCATCCGGCAATCTCTTTAGCCTGCGCTTTTAACTCGTCTGGCAATGCCGGAAGCTGTTTCCCCAGCATGATCAACTGGCGATATTTATCTTCCCATTGCGTGAACGGTGCGAAGGTATTGCGTAACGTTTCTGCGGTTACGGTTGTGCCGAACGGATGTCCGGCGAATTGCGGGTTTGTCATTAATCCACCAATAATTCCAGCGCGCGGTCAACGG

[yangao07]

Actually, the output you show here is the expected format for "-f 2".

[mcrone]

It just doesn't have the number of repeats and all of the other information? It was also not filtering according to the -m tag, there were many results less than 1kb.

[yangao07]

The other information are omitted because you specified "-u", which only output the repeat unit sequence.