Chris Smith

It's tab delimited. Here are the first two identified with signal peptides. # SignalP-6.0 Organism: Eukarya Timestamp: 20211008163009 # ID Prediction OTHER SP(Sec/SPI) CS Position FUN_000010-T1_FUN_000010 SP 0.000237 0.999737 CS...

[signalp.results.txt](https://github.com/nextgenusfs/funannotate/files/7318426/signalp.results.txt)

Hiya, I've found time again to work on this, I just pulled the new master branch and had a go, I've hit a new error. : Existing SignalP results found:...

Heya, looks like it's sort of worked. There appear to be a handful of entries it cannot parse. See below for the output. Existing SignalP results found: Predict/annotate_misc/signalp.results.txt signalP parse...

Oh, also, I get this when I try to include phobius results. Seems to be some sort of clash. I've run this directly after my last test using --phobius phobius.results.txt...

Hey Jon, I'm having the same problem as this. I downloaded from SRA using the command on the Trinity site that you suggested. I'm using the latest version of Funannotate...

SRA download command: fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files SRR13498932 The raw output from that doesn't work. Following which I tried: BBtools repair.sh Which resulted in output that looked like this but...

That appears to have done the job, thanks man! ----Edit---- I spoke too soon. I'm now getting this from the funannotate-train.log R1 header: SRR13498932.1 1/1 and R2 header: SRR13498932.1 1/1...

They look like theyve got the same number of reads in each. Here is the tail SRR13498932_1.repaired.fastq

That's done it, it's progressed through to read normalization now. Thank you so much for taking the time to dig into this and figure it out.