How to handle paired-end reads

[bheimbu]

Hi @sandragodinhosilva

I've tried your workflow with my paired-end read data. In order to use my reads, I've concatenated them. However, I'm wondering whether your workflow excepts forward and reverse reads separated in two files?

Actually, my concatenated fastq file runs, but the workflow seems to be stuck here

[13:37:01] Deleting unwanted file: results/Annotation/BEC323.HAMAP.hmm.tmp.30592.hmmer3
[13:37:08] Labelling remaining 758 proteins as 'hypothetical protein'
[13:37:19] Found 0 unique /gene codes.
[13:37:19] Fixed 0 colliding /gene names.
[13:37:19] Adding /locus_tag identifiers
[13:37:24] Assigned 4199 locus_tags to CDS and RNA features.
[13:37:24] Writing outputs to results/Annotation/
[13:44:20] Generating annotation statistics file
[13:44:37] Generating Genbank and Sequin files
[13:44:37] Running: tbl2asn -V b -a r10k -l paired-ends -M b -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z results\/Annotation\/BEC323\.err -i results\/Annotation\/BEC323\.fsa 2> /dev/null

There is no progress since yesterday afternoon.

Cheers Bastian