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oschwengers avatar oschwengers commented on June 14, 2024

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?

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jennahamlin avatar jennahamlin commented on June 14, 2024

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...

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oschwengers avatar oschwengers commented on June 14, 2024

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...

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jennahamlin avatar jennahamlin commented on June 14, 2024

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

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