Workflow execution completed unsuccessfully! Error executing process > 'calling_pipeline:medakaNetwork (2)'

[Lenfera]

Ask away!

Hello Epi2me labs team,

We tried to run the workflow 'bacterial genome' within an oracle VM with Ubuntu 22.04.3 LTS 64-bit in the Epi2me labs desktop application. To check if it works, we tried 'Use Demo Data'

We had this report :

Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 134.

The full error message was:

Error executing process > 'calling_pipeline:medakaNetwork (2)'

Caused by: Process calling_pipeline:medakaNetwork (2) terminated with an error exit status (134)

Command executed:

medaka --version echo r1041_e82_400bps_sup_v4.2.0

  echo r1041_e82_400bps_sup_v4.2.0

  medaka consensus align.bam "test1.consensus_probs.hdf"         --threads 2 --regions "NC_000962.3:999000-1999000

" --model r1041_e82_400bps_sup_v4.2.0

Command exit status: 134

Command output: medaka 1.9.1 r1041_e82_400bps_sup_v4.2.0 r1041_e82_400bps_sup_v4.2.0

Command error: Cannot import pyabpoa, some features may not be available. medaka 1.9.1 r1041_e82_400bps_sup_v4.2.0 r1041_e82_400bps_sup_v4.2.0 The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine. .command.sh: line 8: 90 Aborted (core dumped) medaka consensus align.bam "test1.consensus_probs.hdf" --threads 2 --regions "NC_000962.3:999000-1999000 " --model r1041_e82_400bps_sup_v4.2.0

Work dir: /home/sprzto/epi2melabs/instances/wf-bacterial-genomes_01HBGHJP7JQSFKRC9P6QD7WTJK/work/72/fb42aff10d6ba33fdc644968b2c3ff

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

I tried this : https://github.com/tensorflow/tensorflow/issues/24548 (mehdirezaie commented on Mar 27, 2020)

But we still have the same error. What could we do to solve this ?

[cjw85]

Please reopen this issue using the more appropriate Bug Report issue template. It helps us to help you.