RaGOO failed Mapping short reads with minimap2 -- RuntimeWarning: Mean of empty slice

Hi @malonge,

I was trying to scaffold an assembly using your great tool. However I keep getting this warning and the minimap2 mapping is not done all.

Here is the command I ran using python3 :

python ../ragoo.py -b -R PE.inter.fq -T sr -t 100 -g 250 -C ../6000flye.ctg.fa ../PFLA.genome.fasta

And here the error-message

nkal/anaconda3/bin/minimap2 6000flye.ctg.fa  PFLA.genome.fasta 
Sun Jul 28 19:44:09 2019 --- Misassembly correction has been turned on. This automatically inactivates chimeric contig correction.
Sun Jul 28 19:44:09 2019 --- Reading alignments
Sun Jul 28 19:44:09 2019 --- Aligning raw reads to contigs
Sun Jul 28 19:44:09 2019 --- Computing contig coverage
/home/nguinkal/anaconda3/envs/mypython3/lib/python3.7/site-packages/numpy-1.17.0-py3.7-linux-x86_64.egg/numpy/core/fromnumeric.py:3257: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/home/nguinkal/anaconda3/envs/mypython3/lib/python3.7/site-packages/numpy-1.17.0-py3.7-linux-x86_64.egg/numpy/core/_methods.py:161: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)

Best, Julien

[malonge]

Thanks - yes sorry for the inconvenience. This is one of the top things on my TODO list since it is much more convenient to be able to provide a path.

[bbalog87]

Hi @malonge, It seems to work now, since minimap2 is running for more than 1h, which has not happened before. Making a symbolic link of the PE-reads within the the same directory as ragoo.py might have fixed the issue. Thank you very much for the prompt and helpful support. Best, Julien