"we have a broken Arrow" about pbbioconda

[pb-dseifert]

pbcoretools is not a meta package and doesn't include Arrow. genomicconsensus is the package you are looking for.

[peterthorpe5]

Still the same error with genomicconsensus installed. If this error anything to worry about? Output freezes half way through outputting the gff and doesnt complete the scaffold list:
##sequence-region scaffold179 1 15375
##sequence-region scaffold18 1 1406724
##sequence-region scaffold180 1 14911
##sequence-region s (freezes here)

conda install genomicconsensus
Solving environment: done

All requested packages already installed.

conda update genomicconsensus
Solving environment: done

# All requested packages already installed.

arrow sorted_mini.pb.bam --diploid --log-file miniarrow.log -j $THREADS --referenceFilename Gpal_newton_final_unpolished.fasta -o ${PREFIX}.arrow${ITERNUM}.fasta -o ${PREFIX}.arrow${ITERNUM}.gff -o ${PREFIX}.arrow${ITERNUM}.fastq

/shelf/apps/pjt6/conda/envs/pb_toolkit/lib/python2.7/site-packages/h5py/init.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._conv import register_converters as _register_converters
/shelf/apps/pjt6/conda/envs/pb_toolkit/lib/python2.7/site-packages/h5py/init.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import h5a, h5d, h5ds, h5f, h5fd, h5g, h5r, h5s, h5t, h5p, h5z
/shelf/apps/pjt6/conda/envs/pb_toolkit/lib/python2.7/site-packages/h5py/_hl/group.py:22: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from .. import h5g, h5i, h5o, h5r, h5t, h5l, h5p

[pb-dseifert]

try installing numpy from conda-forge by adjusting your channel priorities https://bioconda.github.io/#set-up-channels In general those errors are innocuous though

[peterthorpe5]

yes that removed the errors.

Thanks, Pete