Flye error

[juansearch]

Dear Athena, I am running Athena-meta on linked-read data through a docker. I started the run, everything seems to be running OK but then it crashes with the following error:

2019-02-09 12:34:10 - Command 'flye --subassemblies ./results/olc/flye-input-contigs.fa --out-dir ./results/olc/flye-asm-1 --genome-size 41031 --threads 64 --min-overlap 1000' returned non-zero exit status 1 Exception in thread Thread-9: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 754, in run self.target(*self.args, **self.kwargs) File "/usr/lib/python2.7/multiprocessing/pool.py", line 389, in _handle_results task = get() TypeError: ('init__() takes at least 3 arguments (1 given)', <class 'subprocess.CalledProcessError'>, ())

Please help, Juan

[abishara]

Hi Juan,

Are you using the docker image abishara/athena-meta-flye-docker?

It's a little hard to tell from the output copied what exactly is going on. Relative to your config.json file can you remove the olc subdirectory with rm -rf ./results/olc, rerun with a single thread (athena-meta --threads 1), and then upload the full log output if it continues to fail?

Thanks! alex

[johnne]

Hi @abishara, I ran into this issue as well. After upgrading flye to version 2.4.2 (which downgrades athena_meta to v. 1.2) athena-meta completes without an error. What was the reason for switching Flye to version 2.3.1?

Cheers, John

[abishara]

Hi @johnne

I switched to version 2.3.1 once I noticed that athena-meta --test failed for flye 2.4.1. To be honest, I'm not quite sure why I didn't stick to 2.4.2 looking back at this, might be oversight. I just ran with flye 2.4.2 and see that athena-meta --test passes.

Can you clarify what error you are observing though? Installing athena_meta versions 1.2 or 1.3 through conda both work for me at the moment.

Thanks, alex