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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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LAI values could not be calculated #515

Open sunshichao0916 opened 3 weeks ago

sunshichao0916 commented 3 weeks ago

Hi Prof. Ou,

 First, EDTA v2.2.0 was used for TE annotation of the NO1 genome assembled with HiFi reads. 
 Then, we calculated the LAI value using the LTR annotation results (LAI software vbeta3.2) with the following command:

LAI -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out  >NO1.LAI.out

 But, I obtained this log, if there are something wrong? Can you give me some suggestions?

Tue Oct 29 09:47:54 CST 2024 Dependency checking: Passed! Tue Oct 29 09:47:54 CST 2024 Calculation of LAI will be based on the whole genome. Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect ra Tue Oct 29 09:47:54 CST 2024 Estimate the identity of LTR sequences in the genome: standard mode Fri Nov 1 14:29:20 CST 2024 The identity of LTR sequences: 93.6700108663731% Fri Nov 1 14:29:20 CST 2024 Calculate LAI:

                            【Error】Intact LTR-RT content (0%) is too low for accurate LAI calculation (min 0.1% required)
                            【Error】 Total LTR sequence content (0%) is too low for accurate LAI calculation (min 5% required)

                            Sorry, LAI is not applicable on the current genome assembly

Best wish, Shichao

oushujun commented 3 weeks ago

Hi Sichao,

It says intact LTR is too few to calculate. Can you double check?

Shujun

On Fri, Nov 1, 2024 at 3:01 AM sunshichao0916 @.***> wrote:

Hi Prof. Ou,

First, EDTA v2.2.0 was used for TE annotation of the NO1 genome assembled with HiFi reads. Then, we calculated the LAI value using the LTR annotation results (LAI software vbeta3.2) with the following command:

LAI -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out >NO1.LAI.out

But, I obtained this log, if there are something wrong? Can you give me some suggestions?

`Parameters: -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out

Tue Oct 29 09:47:54 CST 2024 Dependency checking: Passed! Tue Oct 29 09:47:54 CST 2024 Calculation of LAI will be based on the whole genome. Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect ra Tue Oct 29 09:47:54 CST 2024 Estimate the identity of LTR sequences in the genome: standard mode Fri Nov 1 14:29:20 CST 2024 The identity of LTR sequences: 93.6700108663731% Fri Nov 1 14:29:20 CST 2024 Calculate LAI:

                        【Error】Intact LTR-RT content (0%) is too low for accurate LAI calculation (min 0.1% required)
                        【Error】 Total LTR sequence content (0%) is too low for accurate LAI calculation (min 5% required)

                        Sorry, LAI is not applicable on the current genome assembly.`

Best wish, Shichao

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/515, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NE2HMSEUQU6GZQMU63Z6MROLAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZDQNBWGYZTAOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

sunshichao0916 commented 3 weeks ago

Hi Sichao, It says intact LTR is too few to calculate. Can you double check? Shujun … On Fri, Nov 1, 2024 at 3:01 AM sunshichao0916 @.> wrote: Hi Prof. Ou, First, EDTA v2.2.0 was used for TE annotation of the NO1 genome assembled with HiFi reads. Then, we calculated the LAI value using the LTR annotation results (LAI software vbeta3.2) with the following command: LAI -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out >NO1.LAI.out But, I obtained this log, if there are something wrong? Can you give me some suggestions? Parameters: -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out Tue Oct 29 09:47:54 CST 2024 Dependency checking: Passed! Tue Oct 29 09:47:54 CST 2024 Calculation of LAI will be based on the whole genome. Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect ra Tue Oct 29 09:47:54 CST 2024 Estimate the identity of LTR sequences in the genome: standard mode Fri Nov 1 14:29:20 CST 2024 The identity of LTR sequences: 93.6700108663731% Fri Nov 1 14:29:20 CST 2024 Calculate LAI: 【Error】Intact LTR-RT content (0%) is too low for accurate LAI calculation (min 0.1% required) 【Error】 Total LTR sequence content (0%) is too low for accurate LAI calculation (min 5% required) Sorry, LAI is not applicable on the current genome assembly. Best wish, Shichao — Reply to this email directly, view it on GitHub <#515>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NE2HMSEUQU6GZQMU63Z6MROLAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZDQNBWGYZTAOI . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you Shujun, I downloaded two other high-quality genomes of this species, one assembled for T2T and TE annotated using the same command and software version. However, I get the same log file as above. I wonder if it's species-specific? Next, I'm going to test it with a different species.

Best wish, Shichao

oushujun commented 2 weeks ago

If this is a non-plant, it may not have a lot of LTR elements in it. Please try with an Arabidopsis genome.

Shujun

On Sun, Nov 3, 2024 at 8:14 PM sunshichao0916 @.***> wrote:

Hi Sichao, It says intact LTR is too few to calculate. Can you double check? Shujun … <#m_6052363394742409577_m4745779182403511913> On Fri, Nov 1, 2024 at 3:01 AM sunshichao0916 @.> wrote: Hi Prof. Ou, First, EDTA v2.2.0 was used for TE annotation of the NO1 genome assembled with HiFi reads. Then, we calculated the LAI value using the LTR annotation results (LAI software vbeta3.2) with the following command: LAI -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out >NO1.LAI.out But, I obtained this log, if there are something wrong? Can you give me some suggestions? Parameters: -genome ./data/NO1.genome.fa -intact ./data/NO1.mod.pass.list -all ./data/NO1.mod.out Tue Oct 29 09:47:54 CST 2024 Dependency checking: Passed! Tue Oct 29 09:47:54 CST 2024 Calculation of LAI will be based on the whole genome. Please use the -mono parameter if your genome is a recent ployploid, otherwise high identity between LTR homeologues will overcorrect ra Tue Oct 29 09:47:54 CST 2024 Estimate the identity of LTR sequences in the genome: standard mode Fri Nov 1 14:29:20 CST 2024 The identity of LTR sequences: 93.6700108663731% Fri Nov 1 14:29:20 CST 2024 Calculate LAI: 【Error】Intact LTR-RT content (0%) is too low for accurate LAI calculation (min 0.1% required) 【Error】 Total LTR sequence content (0%) is too low for accurate LAI calculation (min 5% required) Sorry, LAI is not applicable on the current genome assembly. Best wish, Shichao — Reply to this email directly, view it on GitHub <#515 https://github.com/oushujun/EDTA/issues/515>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NE2HMSEUQU6GZQMU63Z6MROLAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZDQNBWGYZTAOI https://github.com/notifications/unsubscribe-auth/ABNX4NE2HMSEUQU6GZQMU63Z6MROLAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZDQNBWGYZTAOI . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you Shujun, I downloaded two other high-quality genomes of this species, one assembled for T2T and TE annotated using the same command and software version. However, I get the same log file as above. I wonder if it's species-specific? Next, I'm going to test it with a different species.

Best wish, Shichao

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/515#issuecomment-2453673443, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGZP7V2FPY6PYEFQ53Z63DBDAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJTGY3TGNBUGM . You are receiving this because you commented.Message ID: @.***>

oushujun commented 2 days ago

any luck?