No output produced

[ValentinaBoP]

Hello!

I'm experiencing some issues with Kraken, basically I don't get any output (the sample works fine though). I previously aligned two genomes with Satsuma (genome_v1 and genome_v2). I would like to feed Kraken with some coordinates on genome_v1 and get the corresponding on genome_v2

alignment: satsuma_summary.chained.out first genome: genome_v2 second genome: genome_v1

chr10   4912115 4912438 lycPyr_scaffold_9       10763482        10763805        1.000000        -
chr10   4912532 4912738 lycPyr_scaffold_9       10763182        10763388        1.000000        -
chr10   4912739 4913423 lycPyr_scaffold_9       10762497        10763181        1.000000        -
chr10   4913424 4913515 lycPyr_scaffold_9       10762405        10762496        1.000000        -
chr10   4913516 4913604 lycPyr_scaffold_9       10762316        10762404        1.000000        -
chr10   4913605 4914028 lycPyr_scaffold_9       10761892        10762315        1.000000        -

config file:

[genomes]
genome_v1 genomes/genome_v1.fasta
genome_v2 genomes/genome_v2.fasta

[pairwise-maps]
genome_v2 genome_v1 syntenies/satsuma_summary.chained.out

gtf file (coordinates that surely aligned to lycPyr7.1, see above alignment):

lycPyr_scaffold_9       protein_coding  CDS     10763482        10763805        .       -       0       gene_id "none"

I run Kraken like this: RunKraken -c genome.config -s genome.gtf -T genome_v2 -S genome_v1

I also tried to swap the source (-S) and target (-T) genomes but I always get an empty file

I wonder if it is just an error in the gtf file format or in the config file. I played a bit around with no success.

Do you have any suggestion?

Thank you very much for the help, Valentina