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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Message: IPyradError: bwa error: None #450

Closed zilaijuand closed 3 years ago

zilaijuand commented 3 years ago

Hello, when I running the step3: ''nohup ipyrad -p params-iptest.txt -s 3 '' Encountered an Error : ipyrad [v.0.9.71] Interactive assembly and analysis of RAD-seq data

Parallel connection | gs31: 56 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:00:01 | indexing reference [####################] 100% 0:00:56 | dereplicating [####################] 100% 0:01:20 | mapping reads

Encountered an Error. Message: IPyradError: bwa error: None Parallel connection closed.

how can I fix it thanks！

isaacovercast commented 3 years ago

Hello, This is almost certainly a memory allocation issue. From a previous issue on the gitter channel:

@brpark29 How much RAM are you allocating? Looks like bwa is crashing, could be lack of resources. If you have 24 cores you will need at LEAST 96GB of RAM. Easiest way to reduce this burden if you don't have enough RAM is to reduce the number of cores you're running on.

https://gitter.im/dereneaton/ipyrad?at=5d714d9232e48c5df242aefe

Either reduce the # of cores or increase memory allocation. Good luck.

zilaijuand commented 3 years ago

Thanks a lot！