[BUG] <PGAP failed, docker exited with rc = 1>

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline

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[BUG] <PGAP failed, docker exited with rc = 1> #211

Closed Kartikj112 closed 2 years ago

Kartikj112 commented 2 years ago

PGAP is not running when I use my own data

I successfully ran the M. genitalium test genome but when I try to run my own genome it says "PGAP failed, docker exited with rc = 1". I have attached the log file and the .yaml files below.

I'm new to this so a little guidance would be helpful.

Thankyou in advance.

Software versions

OS: [Ubuntu 20.04.4 LTS]
Intel® Core™ i7-10700 CPU @ 2.90GHz × 16
64-bit
31.1 GiB
pgap.py --version: 2022-04-14.build6021
docker image version: 20.10.17

input.yaml.txt submol.yaml.txt cwltool.log

azat-badretdin commented 2 years ago

Thank you for your report, Kartik!

the log says:

line 246: CPgapxYamlCtlApplication::Run() --- Unknown organism Kocuria_sp

thibaudnis commented 2 years ago

Hi @Kartikj112 in submol.yaml.text: genus_species: 'Kocuria_sp'. Please try genus_species: 'Kocuria sp.' instead. Thanks! See https://github.com/ncbi/pgap/wiki/Input-Files

Kartikj112 commented 2 years ago

Thank you for your report, Kartik!

the log says:
line 246: CPgapxYamlCtlApplication::Run() --- Unknown organism Kocuria_sp

It worked. Thankyou again for the help.

Kartikj112 commented 2 years ago

Hi @Kartikj112 in submol.yaml.text: genus_species: 'Kocuria_sp'. Please try genus_species: 'Kocuria sp.' instead. Thanks! See https://github.com/ncbi/pgap/wiki/Input-Files

Very helpful. thankyou.