search

oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
66 stars 18 forks source link

abr fails with example data #19

Open jennahamlin opened 3 years ago

jennahamlin commented 3 years ago

Hello -

I set up a Linux virtual machine (4 CPU, 4GB MEM, 100GB disk with CentOS 8.x) to test out your pipeline. I was able to get the example data provided to run (example-lmonocytogenes-4). However, the ABR analysis failed for each isolate. I provide the asap log file and one example standard out file below:

asap.log Listeria_monocytogenes_SRR2982078.std.log

Looking over other issues submitted, it appears this was problematic for another user (#18). Any thoughts or suggestions for how to get the ABR analysis to work?

Thanks

oschwengers commented 3 years ago

Hello Jenna, thanks for using ASA³P. Due to your logs there seems to occur an internal issue with Singularity. I'll try to reproduce this with a fresh local setup. In the meantime, could you please execute the pipeline in debug mode (asap-docker.sh -d ...) and provide the then more detailed log files?

jennahamlin commented 3 years ago

Hi Oliver -

Thanks for the reply. Attached are the outputs from running in debug mode:

asap.log Listeria_monocytogenes_SRR2982078.std.log

I agree the error is something related to singularity...

oschwengers commented 3 years ago

Hello @jennahamlin , sry for the late reply. I'm still trying to figure out what's going on - so far without a hint. But I'm currently thinking of rewriting the technical backbone and to use Bioconda as requested by other users. I hope this will fix this issue. I'll let you know once I've come up with a new release. I'm very sorry that I cannot provide with a short-term solution right now...

jennahamlin commented 3 years ago

@oschwengers - no worries for the late reply; will keep an eye out for when it is available via bioconda.