cnv_ltffinder2gff.pl

[PlantDr430]

Hello,

I am trying to use the cnv_ltffinder2gff.pl and I keep getting this error:

stephenwyka@bspmgenomics:/data/wyka/transposable_elements/LM470$ ../../dawgpaws/scripts/cnv_ltrfinder2gff.pl -i LM470_ltr_finder.txt --gff-ver GFF3 -o LM470_ltrfinder.gff
Use of uninitialized value $ENV{"DP_GFF"} in uc at ../../dawgpaws/scripts/cnv_ltrfinder2gff.pl line 46.

I get the same error even if I don't use the --gff-ver flag

Any idea what could be causing this?

[linshuting]

I got the same problem too, did you solve it?

[PlantDr430]

So I thought I altered something in the script, but when I went to check it I noticed that it wasn't different than the version currently posted. I just re-downloaded the currently posted version and I get the same error and the gff file is not populated. However, when I use a version that I got working (again which I can't find what is actually different) I get the same error, but the gff file is populated.

See below:

I renamed the newly downloaded file to "cnv_ltr.pl", while my version that works has the full name.

stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$ ls -al
total 30768
drwxrwxrwx  2 stephenwyka stephenwyka     4096 Feb 29 18:36 .
drwxrwxrwx 38 stephenwyka stephenwyka     4096 Feb 29 18:36 ..
-rwxrwxrwx  1 stephenwyka stephenwyka    36700 Feb 29 18:35 cnv_ltrfinder2gff.pl
-rwxrwxrwx  1 stephenwyka stephenwyka    36614 Feb 29 18:36 cnv_ltr.pl
-rwxrwxrwx  1 stephenwyka stephenwyka   148261 Feb 29 17:46 LM4_ltr_out
-rwxrwxrwx  1 stephenwyka stephenwyka 31271685 Feb 29 17:44 LM4_masked.fasta

stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$ ./cnv_ltr.pl -i LM4_masked.fasta -o LM4_ltr.gff --gff-ver GFF3
Use of uninitialized value $ENV{"DP_GFF"} in uc at ./cnv_ltr.pl line 46.

stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$ ls -al
total 30772
drwxrwxrwx  2 stephenwyka stephenwyka     4096 Feb 29 18:37 .
drwxrwxrwx 38 stephenwyka stephenwyka     4096 Feb 29 18:36 ..
-rwxrwxrwx  1 stephenwyka stephenwyka    36700 Feb 29 18:35 cnv_ltrfinder2gff.pl
-rwxrwxrwx  1 stephenwyka stephenwyka    36614 Feb 29 18:36 cnv_ltr.pl
-rw-rw-r--  1 stephenwyka stephenwyka       16 Feb 29 18:37 LM4_ltr.gff
-rwxrwxrwx  1 stephenwyka stephenwyka   148261 Feb 29 17:46 LM4_ltr_out
-rwxrwxrwx  1 stephenwyka stephenwyka 31271685 Feb 29 17:44 LM4_masked.fasta

stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$ ./cnv_ltrfinder2gff.pl -i LM4_ltr_out -o LM4_ltr.gff --gff-ver GFF3
Use of uninitialized value $ENV{"DP_GFF"} in uc at ./cnv_ltrfinder2gff.pl line 46.

stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$ ls -al
total 30784
drwxrwxrwx  2 stephenwyka stephenwyka     4096 Feb 29 18:37 .
drwxrwxrwx 38 stephenwyka stephenwyka     4096 Feb 29 18:36 ..
-rwxrwxrwx  1 stephenwyka stephenwyka    36700 Feb 29 18:35 cnv_ltrfinder2gff.pl
-rwxrwxrwx  1 stephenwyka stephenwyka    36614 Feb 29 18:36 cnv_ltr.pl
-rw-rw-r--  1 stephenwyka stephenwyka    12624 Feb 29 18:37 LM4_ltr.gff
-rwxrwxrwx  1 stephenwyka stephenwyka   148261 Feb 29 17:46 LM4_ltr_out
-rwxrwxrwx  1 stephenwyka stephenwyka 31271685 Feb 29 17:44 LM4_masked.fasta
stephenwyka@bspmgenomics:/data/wyka/Old_files_and_directories/TEST$

The populated gff looks like this:

##gff-version 3
contig_33   ltr_finder  LTR_retrotransposon 1579    6411    6   +   .   ID=contig_33_ltr_finder_model0001
contig_33   ltr_finder  five_prime_LTR  1579    2616    6   +   .   ID=contig_33_ltr_finder_model0001_five_prime_LTR;Name=Five Prime LTR;Parent=contig_33_ltr_finder_model0001
contig_33   ltr_finder  three_prime_LTR 5337    6411    6   +   .   ID=contig_33_ltr_finder_model0001_three_prime_LTR;Name=Three Prime LTR;Parent=contig_33_ltr_finder_model0001
contig_33   ltr_finder  RR_tract    5322    5336    6   +   .   ID=contig_33_ltr_finder_model0001_RR_tract;Name=PPT;Parent=contig_33_ltr_finder_model0001
contig_33   ltr_finder  target_site_duplication 1575    1578    6   +   .   ID=contig_33_ltr_finder_model0001_tsd5;Name=Target Site Duplication;Parent=contig_33_ltr_finder_model0001
contig_33   ltr_finder  target_site_duplication 6412    6415    6   +   .   ID=contig_33_ltr_finder_model0001_tsd3;Name=Target Site Duplication;Parent=contig_33_ltr_finder_model0001
contig_36   ltr_finder  LTR_retrotransposon 62646   65673   6   +   .   ID=contig_36_ltr_finder_model0001
contig_36   ltr_finder  five_prime_LTR  62646   62964   6   +   .   ID=contig_36_ltr_finder_model0001_five_prime_LTR;Name=Five Prime LTR;Parent=contig_36_ltr_finder_model0001
contig_36   ltr_finder  three_prime_LTR 65355   65673   6   +   .   ID=contig_36_ltr_finder_model0001_three_prime_LTR;Name=Three Prime LTR;Parent=contig_36_ltr_finder_model0001
contig_36   ltr_finder  RR_tract    65289   65303   6   +   .   ID=contig_36_ltr_finder_model0001_RR_tract;Name=PPT;Parent=contig_36_ltr_finder_model0001
contig_36   ltr_finder  target_site_duplication 62641   62645   6   +   .   ID=contig_36_ltr_finder_model0001_tsd5;Name=Target Site Duplication;Parent=contig_36_ltr_finder_model0001
contig_36   ltr_finder  target_site_duplication 65674   65678   6   +   .   ID=contig_36_ltr_finder_model0001_tsd3;Name=Target Site Duplication;Parent=contig_36_ltr_finder_model0001

While the unpopulated verion just has the ##gff-version 3 header and that's all.

I'm serious baffled as why this particular copy works (attached, with a .txt extension) as I can't find any differences between them. I also got this to work like a year and a half ago when I was still learning so I didn't document how I got it working, sorry. Let me know if this version works for you.

Edit: Just tested it on a newly created test_user account on our server and this version of the script worked.

cnv_ltrfinder2gff.pl.txt

[linshuting]

I really appreciate your help. However, I keep getting the same error even used .txt version. I'm really confused as to why this is happening. Thanks again anyway!

[PlantDr430]

Ah, sorry it didn't work. I tested it on personal laptop and got it working so that suggest that it works somewhere else besides our main server. I am also confused as to what is causing the error and why I can get it to work with a particular saved version.

I use this script in one of my pipelines, but since it's not really working I will probably remove it and create my own parser. It won't have the same functionalities as this script (i.e. merging multiple gffs) as I only need to run it once and extract a single gff. It shouldn't be hard to create and I could let you know when the parser is finished if all you need is to just turn the LTR_finder output into 1 gff file.

[PlantDr430]

@linshuting

If you just need LTR_finder output to GFF3, this should do the trick. https://github.com/PlantDr430/CSU_scripts/blob/master/ltr_finder_2gff.py

[linshuting]

OMG! It works, thanks a ton!!!!!

[PlantDr430]

@linshuting

No worries, if you have any issue please post them to my GitHub page.