FORUMgtfToGenePred module unknown
Victoria asked 11 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It is also possible your cache file is out-of-date; it may help to try: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 11 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 11 months ago

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

zhibin Staff replied 11 months ago

You can try

chmod +x ./gtfToGenePred
./gtfToGenePred

Victoria replied 11 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 11 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 11 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 11 months ago

Go inside the directory and do

chmod +x ./gtfToGenePred
./gtfToGenePred

Or use the full path.

Victoria replied 11 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 11 months ago

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

Victoria replied 11 months ago

That worked! thank you!!

flefebvre Staff answered 11 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