LAI values could not be calculated

[sunshichao0916]

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]

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: ***@***.***>

[sunshichao0916]

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]

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_m_4745779182403511913_> 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 <#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 <#515 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NGZP7V2FPY6PYEFQ53Z63DBDAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJTGY3TGNBUGM> . You are receiving this because you commented.Message ID: ***@***.***>

[oushujun]

any luck?

[sebeier]

I had the same issue. The instructions on the LAI help can be a little misleading, you need to point towards the .fa.mod file instead of the .fa. The actual command will be: LAI -genome <genome>.fa.mod -intact <genome>.fa.mod.EDTA.raw/LTR/<genome>.fa.mod.pass.list -all <genome>.fa.mod.EDTA.anno/<genome>.fa.mod.out

[oushujun]

That’s correct! All analysis should be based on the same file. Here, LTR annotations were based on the fa.mod file not the original .fa file. Shujun

…

On Tue, Jan 21, 2025 at 4:41 AM Sebastian Beier ***@***.***> wrote: I had the same issue. The instructions on the LAI help can be a little misleading, you need to point towards the .fa.mod file instead of the .fa. The actual command will be: LAI -genome <genome>.fa.mod -intact <genome>.fa.mod.EDTA.raw/LTR/<genome>.fa.mod.pass.list -all <genome>.fa.mod.EDTA.anno/<genome>.fa.mod.out — Reply to this email directly, view it on GitHub <#515 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NFVM3WYVX4SKDR4XTT2LYI4NAVCNFSM6AAAAABQ7YQAEKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMBUGE3TSNJRGM> . You are receiving this because you commented.Message ID: ***@***.***>