FORUMgtfToGenePred module unknown
Victoria asked 2 months ago



Hi all,
I’m trying to load the module gtfToGenePred and I keep getting an error:
$ module load gtfToGenePred
Lmod has detected the following error: The following module(s) are unknown: “gtfToGenePred”
Please check the spelling or version number. Also try “module spider …”
It is also possible your cache file is out-of-date; it may help to try:
$ module –ignore-cache load “gtfToGenePred”
Also make sure that all modulefiles written in TCL start with the string #%Module

But the module is listed in my directory and when I try to download it again it says
The file is already fully retrieved; nothing to do.
I have also tried module spider and it says Unable to find: “gtfToGenePred”
Is there some other module I need to load with it?

2 Answers
zhibin Staff answered 2 months ago



I do not think there is a module for it. You can download from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred and use it directly.

Victoria replied 2 months ago

I have downloaded this but when I try to execute it says command not found

zhibin Staff replied 2 months ago

You can try

chmod +x ./gtfToGenePred
./gtfToGenePred

Victoria replied 2 months ago

I have also done that and I get back
-bash: ./gtfToGenePred: Is a directory
But still says command not found when I try to execute

zhibin Staff replied 2 months ago

Are you should you download it correctly or did you put the downloaded file to its own directly? “gtfToGenePred” should be the file you downloaded.

Victoria replied 2 months ago

“gtfToGenePred” is listed under my tools directory as a directory and within that, there are two files: “gtfToGenePred” and “genePredToBed” should theis only be a single file and not a directory?

zhibin Staff replied 2 months ago

Go inside the directory and do

chmod +x ./gtfToGenePred
./gtfToGenePred

Or use the full path.

Victoria replied 2 months ago

Sorry this is long but I copied and pasted so you can see..Either way I do it it’s not working

vrea@gra-login3:~/scratch/rnaseq/student_tools$ ./gtfToGenePred
-bash: ./gtfToGenePred: Is a directory
vrea@gra-login3:~/scratch/rnaseq/student_tools$ cd gtfToGenePred
vrea@gra-login3:~/scratch/rnaseq/student_tools/gtfToGenePred$ chmod +x ./gtfToGenePred
chmod: cannot access ‘./gtfToGenePred’: No such file or directory
vrea@gra-login3:~/scratch/rnaseq/student_tools/gtfToGenePred$ ./gtfToGenePred
-bash: ./gtfToGenePred: No such file or directory

Then I tried removing it and starting again in the directory where my gtf file is and it says its saved but still wont work

2020-06-23 11:07:38 (11.9 MB/s) – ‘gtfToGenePred’ saved [25700696/25700696]

vrea@gra-login3:~/scratch/rnaseq/refs$ gtfToGenePred Danio_rerio.GRCz11.100.gtf Danio_rerio.GRCz11.100.genePred
-bash: gtfToGenePred: command not found
vrea@gra-login3:~/scratch/rnaseq/refs$ chmod +x ./gtfToGenePred
vrea@gra-login3:~/scratch/rnaseq/refs$ ./gtfToGenePred
gtfToGenePred – convert a GTF file to a genePred
usage:
gtfToGenePred gtf genePred

options:
-genePredExt – create a extended genePred, including frame
information and gene name
-allErrors – skip groups with errors rather than aborting.
Useful for getting infomation about as many errors as possible.
-ignoreGroupsWithoutExons – skip groups contain no exons rather than
generate an error.
-infoOut=file – write a file with information on each transcript
-sourcePrefix=pre – only process entries where the source name has the
specified prefix. May be repeated.
-impliedStopAfterCds – implied stop codon in after CDS
-simple – just check column validity, not hierarchy, resulting genePred may be damaged
-geneNameAsName2 – if specified, use gene_name for the name2 field
instead of gene_id.
-includeVersion – it gene_version and/or transcript_version attributes exist, include the version
in the corresponding identifiers.
vrea@gra-login3:~/scratch/rnaseq/refs$ gtfToGenePred Danio_rerio.GRCz11.100.gtf Danio_rerio.GRCz11.100.genePred
-bash: gtfToGenePred: command not found

zhibin Staff replied 2 months ago

You can try “~/scratch/rnaseq/refs/gtfToGenePred Danio_rerio.GRCz11.100.gtf Danio_rerio.GRCz11.100.genePred”

Victoria replied 2 months ago

That worked! thank you!!

flefebvre Staff answered 2 months ago



Hi Victoria, gtfToGenePred is available through the kentutils module:

module load nixpkgs/16.09 gcc/7.3.0 kentutils/20180716
gtfToGenePred

It is also available through the mugqic stack under the mugqic/ucsc modules:
 

export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
module use $MUGQIC_INSTALL_HOME/modulefiles
module load mugqic/ucsc/v387
gtfToGenePred