Scripts get killed

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Scripts get killed

Shamika Mohanan
Hello,

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?

Regards,
Shamika

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Re: Scripts get killed

nathandunn


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. 

Nathan


On Nov 16, 2020, at 7:49 AM, Shamika Mohanan <[hidden email]> wrote:

Hello,

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.

Are you talking about using flatfile-to-json.pl. ? 

Can you post the command you ran and the output and any other relevant details?  


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? 

Same as above.  This is a jbrowse command.


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?

Not sure.  My guess is that it has to do with Perl libraries.   I’ve run these using docker on the Mac as getting perl to function properly there is such a pain. 

That being said, I’ve mostly been working in PIP.  You might try loading GFF3 from here instead as we’ve been more actively maintaining that:


Nathan


Regards,
Shamika


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