Errors when running ucsc-to-json.pl script

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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

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Re: Errors when running ucsc-to-json.pl script

nathandunn
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., 




Nathan


On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <[hidden email]> wrote:

Hello,

When trying to load data from 
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

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Re: Errors when running ucsc-to-json.pl script

Shamika Mohanan
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

On 16/11/2020 16:35, Nathan Dunn wrote:
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., 




Nathan


On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <[hidden email]> wrote:

Hello,

When trying to load data from 
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


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Re: Errors when running ucsc-to-json.pl script

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

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

On Tue, Nov 17, 2020 at 5:55 AM smm <[hidden email]> wrote:
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

On 16/11/2020 16:35, Nathan Dunn wrote:
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., 




Nathan


On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <[hidden email]> wrote:

Hello,

When trying to load data from 
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


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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].

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