Errors when running ucsc-to-json.pl script

[Shamika Mohanan]

Hello,

When trying to load data from 

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ 

using Apollo-2.6.1/bin/ucsc-to-json.pl script, I get errors like 

Cannot convert gwipsvizRiboseq track; this script is not capable of handling bigWig tracks.

(or)

Cannot convert phyloP100way track; this script is not capable of handling wig tracks.

(or)

Cannot convert mrna track; this script is not capable of handling psl tracks.

(or)

couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files

 at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 286.

 at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.

Bio::JBrowse::ConfigurationManager::__ANON__("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a} at /"...) called at /usr/share/perl/5.22/Carp.pm line 166

Carp::croak("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a}") called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm line 98

Bio::JBrowse::ExternalSorter::finish(Bio::JBrowse::ExternalSorter=HASH(0x2e4efe0)) called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 286

The final error was seen when loading a large file. Is there a way to get past these errors?

Regards,

Shamika

[Nathan Dunn]

If you type in the 

ulimit -n

command what do you see? 

My guess is that this needs to be upped.  Ulimit -n 10000 e.g., 

http://gmod.827538.n3.nabble.com/Gmod-ajax-restrict-zoom-level-tp4042205p4043034.html

Nathan

[smm]

Hello,

Thanks. I have increased ulimit as suggested. I will let you know if it worked. In the meantime, running these commands raise an error-

~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc --track mrna --out dest_loc

Cannot convert mrna track; this script is not capable of handling psl tracks.

 at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
    Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert mrna track; this script is not capable of hand"...) called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 202

~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc --track phyloP100way --out dest_loc

Cannot convert phyloP100way track; this script is not capable of handling wig tracks.

 at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
    Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert phyloP100way track; this script is not capable"...) called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 202

I have downloaded the .sql and .txt files from here- http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/. Please let me know if I should set some flag or if there is some other way to load UCSC MySQL database.

Regards,
Shamika

[Colin]

In general ucsc-to-json doesn't have the capability to load all types of tracks from the UCSC database

For the phyloP i'd use a bigwig file

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/

For the mrna track that gives a PSL error, I am not sure which track this refers to as no track is named mrna in the UCSC database there (e.g. no mrna.sql or mrna.txt.gz)

If needed though, probably would need to convert the PSL to some gff type thing or bigBed, similar to the other thread. bigPsl is an option, it is just a particular type of bigBed, and then load as bigBed (won't display all the alignments in the PSL but might help enough)

-Colin

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