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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Invalid value for shared scalar #153

Closed SamCT closed 11 months ago

SamCT commented 1 year ago

Hello,

I'm trying the new install of LTR_retriever (2.9.4), and am getting an error, related to issue #104 :

Invalid value for shared scalar at /nfsX/LAB/usr/conda/LTR/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 2048.
Thu May 11 09:16:46 PDT 2023    Intact LTR-RT found: 0

And in the error file of the SGE_Batch:

Invalid value for shared scalar at /nfsX/LAB/usr/conda/LTR/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 2048.
cp: cannot stat 'genome.fasta.retriever.scn.adj': No such file or directory

This error is the same whether I am using the conda env install, or a manual install with pathways specified in the paths file. Goal here was just to test whether the new version of retriever had a significant difference in LAI (I expect probably not?, but am curious).

I get a successful run on the old version of LTR_retriever (2.9.0). To be clear I am following the pipeline specified in this github (suffixerator -> harvest -> LTR_paralellize -> *genome.fa.rawLTR.scn -> LTR_retriever). Tried rerunning the pipeline fresh to see if it was an issue related to old files and that doesn't seem to be related.

How might I be able to resolve this error and move forward with testing the new version of LTR_retriever?

Thank you

oushujun commented 1 year ago

That's a weird error (I don't remember I see this error before). Checked line 114 and there is only one variable: $scn{$id}[12], which is the 13th column of the *genome.fa.rawLTR.scn file. You may want to check the scn file and see if there's any abnormality. If you can invoke the new LTR_retriever, that means the installation is good. Issue #104 seems to be not related. Did you check the program with the small test file?

Shujun

SamCT commented 1 year ago

By small test file, do you mean the dummb060817.fa within the database folder? I've tried that -- says no candidate is found (for both v2.9.0 and 2.9.4). For both instances the "Dependency checking: ALL passed!". Not sure if this is the correct test you are referring to.

And I think the .scn file is okay, considering I was able to properly generate an LAI index using LTR_retriever 2.9.0. Just finished another run successfully last night with that version.

Here is the first 4 lines of my *genome.fa.rawLTR.scn file (I'm actually not seeing a 13th column?):


192080  202500  10421  192080  192399  320  202166  202500  335  88.96  0
309366  311693  2328  309366  309939  574  311106  311693  588  96.77  0
432534  440037  7504  432534  434109  1576  438458  440037  1580  97.85  0
oushujun commented 1 year ago

There's link to a small file in #104

On Fri, May 12, 2023 at 11:30 AM Sam Talbot @.***> wrote:

By small test file, do you mean the dummb060817.fa within the database folder? I've tried that -- says no candidate is found (for both v2.9.0 and 2.9.4). For both instances the "Dependency checking: ALL passed!". Not sure if this is the correct test you are referring to.

And I think the .scn file is okay, considering I was able to properly generate an LAI index using LTR_retriever 2.9.0. Just finished another run successfully last night with that version.

Here is the first 4 lines of my *genome.fa.rawLTR.scn file (I'm actually not seeing a 13th column?):

192080 202500 10421 192080 192399 320 202166 202500 335 88.96 0 309366 311693 2328 309366 309939 574 311106 311693 588 96.77 0 432534 440037 7504 432534 434109 1576 438458 440037 1580 97.85 0`

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SamCT commented 1 year ago

Running with the test genome.fa within the EDTA test files and I have the same issue using LRT_retriever version 2.9.4:

gt suffixerator -db genome.fa -indexname genome.fa -tis -suf -lcp -des -ssp -sds -dna

gt ltrharvest -index genome.fa -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes > test.fa.harvest.scn

LTR_FINDER_parallel -seq genome.fa -harvest_out -size 1000000 -time 300

cat genome.fa.harvest.scn genome.fa.finder.combine.scn > genome.fa.rawLTR.scn

LTR_retriever -genome genome.fa -inharvest genome.fa.rawLTR.scn

Sun May 14 05:14:58 PDT 2023 Dependency checking: All passed! Sun May 14 05:15:12 PDT 2023 LTR_retriever is starting from the Init step. Sun May 14 05:15:12 PDT 2023 Start to convert inputs... Total candidates: 12 Total uniq candidates: 12

Sun May 14 05:15:12 PDT 2023 Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded.

Sun May 14 05:15:12 PDT 2023 12 clean candidates remained

Sun May 14 05:15:12 PDT 2023 Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step.

/your_path_to/LTR_retriever -genome genome.fa -inharvest genome.fa.rawLTR.scn Invalid value for shared scalar at /Lab/Usr/bin/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 11. Sun May 14 05:15:31 PDT 2023 Intact LTR-RT found: 0

cp: cannot stat 'genome.fa.retriever.scn.adj': No such file or directory Sun May 14 05:15:31 PDT 2023 No LTR-RT was found in your data.

ricardo-aaron commented 1 year ago

I'm having the same issue with v2.9.4, tried two genomes, both output this: Parameters: -genome genome_clean.fasta -inharvest genome.rawLTR.scn -threads 24 -noanno Mon 19 Jun 2023 08:57:56 AM CDT Dependency checking: All passed! Mon 19 Jun 2023 08:58:01 AM CDT LTR_retriever is starting from the Init step. Mon 19 Jun 2023 08:58:03 AM CDT Start to convert inputs... Total candidates: 599 Total uniq candidates: 558 Mon 19 Jun 2023 08:58:04 AM CDT Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded. Mon 19 Jun 2023 08:58:05 AM CDT 558 clean candidates remained Mon 19 Jun 2023 08:58:05 AM CDT Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step. Invalid value for shared scalar at /castle/rchavez/micromamba/envs/ltr_retriever/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 88. Mon 19 Jun 2023 08:58:29 AM CDT Intact LTR-RT found: 0 cp: cannot stat 'genome_clean.fasta.retriever.scn.adj': No such file or directory Mon 19 Jun 2023 08:58:29 AM CDT No LTR-RT was found in your data. Mon 19 Jun 2023 08:58:29 AM CDT All analyses were finished!

oushujun commented 1 year ago

Yeah there is a bug in v2. 9. 4, You may use the v2. 9. 0 for now.

shujun

On Mon, Jun 19, 2023 at 10:07 AM Ricardo A. Chávez Montes < @.***> wrote:

I'm having the same issue with v2.9.4, tried two genomes, both output this: Parameters: -genome genome_clean.fasta -inharvest genome.rawLTR.scn -threads 24 -noanno Mon 19 Jun 2023 08:57:56 AM CDT Dependency checking: All passed! Mon 19 Jun 2023 08:58:01 AM CDT LTR_retriever is starting from the Init step. Mon 19 Jun 2023 08:58:03 AM CDT Start to convert inputs... Total candidates: 599 Total uniq candidates: 558 Mon 19 Jun 2023 08:58:04 AM CDT Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded. Mon 19 Jun 2023 08:58:05 AM CDT 558 clean candidates remained Mon 19 Jun 2023 08:58:05 AM CDT Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step. Invalid value for shared scalar at /castle/rchavez/micromamba/envs/ltr_retriever/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 88. Mon 19 Jun 2023 08:58:29 AM CDT Intact LTR-RT found: 0 cp: cannot stat 'genome_clean.fasta.retriever.scn.adj': No such file or directory Mon 19 Jun 2023 08:58:29 AM CDT No LTR-RT was found in your data. Mon 19 Jun 2023 08:58:29 AM CDT All analyses were finished!

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oushujun commented 12 months ago

Hello all,

This bug should be fixed in the latest version. Please update and run again. Let me know if you still have the issue.

Thanks! Shujun

SamCT commented 11 months ago

Fixed! Thank you Shujun!

ghost commented 3 months ago

Hello all,

This bug should be fixed in the latest version. Please update and run again. Let me know if you still have the issue.

Thanks! Shujun

Hi Dr.Shujun, so much thanks for writing this fascinating program!

I've noticed that the Invalid value bug of LTR_retriever v2.9.4 is still presenting nowadays while I installed EDTA via conda and downgrading the version of LTR_retriever from 2.9.4 to 2.9.0 helps to fix this issue indeed.

Best, Yanyang.

oushujun commented 3 months ago

Hi yangyang,

The latest version is 2.9.9. https://anaconda.org/bioconda/ltr_retriever

THanks, SHujun