1. Is there a nice way to handle loading really large data files? When trying to load ftp://ftp.ensembl.org/pub/release-101/regulation/homo_sapiens/MotifFeatures/Homo_sapiens.GRCh38.motif_features.gff.gz the process gets killed.
2. When running Apollo-2.6.1/bin/generate-names.pl, the process gets killed. The script used to work earlier but now it gets killed. Is this because size of data it now has to process?
3. When running Apollo-2.6.1/tools/data/add_features_from_gff3_to_annotations.pl, the process gets killed. This script has never worked. Is there a specific reason the process would be killed?
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Going cross-post to the JBrowse list for questions 1 and 2 and answer what I can in-line.
In general, there may be issues with the way the perl libraries are included.
It might work better using the jbrowse/bin instead or just downloading JBrowse separately to run the commands http://github.com/GMOD/jbrowse after running the setup script (should be identical in the Apollo-2.6.1/jbrowse/bin directory) , but I am just guessing.