Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129 about ltr_retriever

[wlhCNU]

My genome Chromosome ID were shown followed:

Chr01
Chr10
Chr11
Chr12
Chr13
Chr14
Chr15
Chr16
Chr17
Chr18
Chr19
Chr02
Chr20
Chr03
Chr04
Chr05
Chr06
Chr07
Chr08
Chr09

[MoradMMokhtar]

Hello Ou： I have two questions to need you help. The first one :

when I run the LTR_retriever, I met a lot of same error messages lines as follow: substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129. substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129. substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129. substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129. substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129. substr outside of string at call_seq_by_list.pl line 128. Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129

When I manual run the call_seq_by_list.pl, using the follow command lines: perl call_seq_by_list.pl genome.fasta.retriever.scn.full -C genome.fasta > ltrTE.fa In addition to get the same as above error messeges, I also found some ltrTE.fa result line is emply, for example:

Chr02:99911289..99791824|Chr02:99911289..99918781

Chr02:99978658..99791824|Chr02:99978658..99989418

Chr02:99993211..99791824|Chr02:99993211..100003060

Chr02:100005808..99791824|Chr02:100005808..100015472

Chr02:100028374..99791824|Chr02:100028374..100041986

Chr02:100081604..99791824|Chr02:100081604..100092164

Chr02:100103379..99791824|Chr02:100103379..100113164

Chr02:100160631..99791824|Chr02:100160631..100170165

The length of my genome Chr02 is 99791824. What doubt to me is that : the start pos is large than the length of Chr02(for example Chr02:99911289..99791824|Chr02:99911289..99918781).

The second question is : In the directory RM_716953.ThuDec12115012022 , a lot error messages log files were create and the error message is that : ncResults-1669900505-717007.err BLAST engine error: Empty CBlastQueryVector

My genome have 20 chromosomes, but in the result genome.fasta.pass.list.gff3,only Chr01 and Chr02 have Identified LTR result information, while the other 18 chomosome fail to identified LTR result.

Thanks

Dear wlhCNU
I have the same issue did you find a solution?

[oushujun]

Hello @wlhCNU @MoradMMokhtar,

You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue.

Best,
Shujun

[MoradMMokhtar]

Hello @wlhCNU @MoradMMokhtar,

You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue.

Best, Shujun

Dear @oushujun
Thank you for your reply, I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever. Maybe it is because of the Id length more than 15 characters "JAEFBJ010000014.1"

[oushujun]

Can you please try again?

…

On Sat, Dec 3, 2022 at 4:41 PM MoradMMokhtar ***@***.***> wrote: Hello @wlhCNU <https://github.com/wlhCNU> @MoradMMokhtar <https://github.com/MoradMMokhtar>, You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue. Best, Shujun Dear @oushujun <https://github.com/oushujun> Thank you for your reply, I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever. Maybe it is because of the Id length more than 15 characters "JAEFBJ010000014.1" — Reply to this email directly, view it on GitHub <#140 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[wlhCNU]

Hello @oushujun @MoradMMokhtar ,
It is right that two different versions of genomes were wrong used. The reason for this problem is that the genome were splited single chrome sequence to run ltr_finder analysis parallelly to save running time. But I ignored combine the ltr_finder result with the input genome chromosome order. But in LTR_retriever analysis process, convert_ltr_finder.pl need the right order input ltr_finder combine result, otherwise it will result in " call_seq_by_list.pl line 129" error messages.
In the original ltr_finder result have the cleary chromosome information,for example ">Sequence: Chr01 Len:111624253" in my ltr_finder result. It is better if convert_ltr_finder.pl could abstract the chromoseme id directly from original ltr_finder result.

Thanks

[MoradMMokhtar]

Can you please try again?
…
On Sat, Dec 3, 2022 at 4:41 PM MoradMMokhtar @.> wrote: Hello @wlhCNU https://github.com/wlhCNU @MoradMMokhtar https://github.com/MoradMMokhtar, You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue. Best, Shujun Dear @oushujun https://github.com/oushujun Thank you for your reply, I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever. Maybe it is because of the Id length more than 15 characters "JAEFBJ010000014.1" — Reply to this email directly, view it on GitHub <#140 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI . You are receiving this because you were mentioned.Message ID: @.>
@oushujun @wlhCNU
Thank you for your reply
I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever for Arabidopsis thaliana and it worked well and the results were good. When I did the same work in Arabidopsis lyrata (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/255/GCF_000004255.2_v.1.0/GCF_000004255.2_v.1.0_genomic.fna.gz), I had the error messages "call_seq_by_list.pl line 128 & 129". I have attached the combined file and the output from LTR_retriever. If you have time, can you please check what is wrong?

LTR_retriever.zip

[oushujun]

You may want to use LTR_FINDER_parallel and LTRharvest_parallel to accelerate your run to get input files. Shujun On Sun, Dec 4, 2022 at 10:03 AM MoradMMokhtar ***@***.***> wrote:

…

Can you please try again? … <#m_6586522269264675891_> On Sat, Dec 3, 2022 at 4:41 PM MoradMMokhtar *@*.*> wrote: Hello @wlhCNU <https://github.com/wlhCNU> https://github.com/wlhCNU <https://github.com/wlhCNU> @MoradMMokhtar <https://github.com/MoradMMokhtar> https://github.com/MoradMMokhtar <https://github.com/MoradMMokhtar>, You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue. Best, Shujun Dear @oushujun <https://github.com/oushujun> https://github.com/oushujun <https://github.com/oushujun> Thank you for your reply, I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever. Maybe it is because of the Id length more than 15 characters "JAEFBJ010000014.1" — Reply to this email directly, view it on GitHub <#140 (comment) <#140 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI <https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI> . You are receiving this because you were mentioned.Message ID: @.*> @oushujun <https://github.com/oushujun> @wlhCNU <https://github.com/wlhCNU> Thank you for your reply I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever for Arabidopsis thaliana and it worked well and the results were good. When I did the same work in Arabidopsis lyrata ( https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/255/GCF_000004255.2_v.1.0/GCF_000004255.2_v.1.0_genomic.fna.gz), I had the error messages "call_seq_by_list.pl line 128 & 129". I have attached the combined file and the output from LTR_retriever. If you have time, can you please check what is wrong? LTR_retriever.zip <https://github.com/oushujun/LTR_retriever/files/10148827/LTR_retriever.zip> — Reply to this email directly, view it on GitHub <#140 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NDAK5VXWHF62XD3OOTWLS6DRANCNFSM6AAAAAASRUH2JI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[MoradMMokhtar]

You may want to use LTR_FINDER_parallel and LTRharvest_parallel to accelerate your run to get input files. Shujun On Sun, Dec 4, 2022 at 10:03 AM MoradMMokhtar @.> wrote:
…
Can you please try again? … <#m_6586522269264675891_> On Sat, Dec 3, 2022 at 4:41 PM MoradMMokhtar @.> wrote: Hello @wlhCNU https://github.com/wlhCNU https://github.com/wlhCNU https://github.com/wlhCNU @MoradMMokhtar https://github.com/MoradMMokhtar https://github.com/MoradMMokhtar https://github.com/MoradMMokhtar, You are likely using different versions of genomes. For example, if you generate the candidate list with the v1 genome and use it on the v2 genome, you will run into this issue. Best, Shujun Dear @oushujun https://github.com/oushujun https://github.com/oushujun https://github.com/oushujun Thank you for your reply, I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever. Maybe it is because of the Id length more than 15 characters "JAEFBJ010000014.1" — Reply to this email directly, view it on GitHub <#140 (comment) <#140 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI https://github.com/notifications/unsubscribe-auth/ABNX4NBNT7EGXA5Y2IKD52LWLPEAFANCNFSM6AAAAAASRUH2JI . You are receiving this because you were mentioned.Message ID: @.> @oushujun https://github.com/oushujun @wlhCNU https://github.com/wlhCNU Thank you for your reply I combined the results from LTR _finder and LTR _harvest and used the same fasta file for LTR_finder, LTR_harvest and LTR_retriever for Arabidopsis thaliana and it worked well and the results were good. When I did the same work in Arabidopsis lyrata ( https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/255/GCF_000004255.2_v.1.0/GCF_000004255.2_v.1.0_genomic.fna.gz), I had the error messages "call_seq_by_list.pl line 128 & 129". I have attached the combined file and the output from LTR_retriever. If you have time, can you please check what is wrong? LTR_retriever.zip https://github.com/oushujun/LTR_retriever/files/10148827/LTR_retriever.zip — Reply to this email directly, view it on GitHub <#140 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDAK5VXWHF62XD3OOTWLS6DRANCNFSM6AAAAAASRUH2JI . You are receiving this because you were mentioned.Message ID: @.**>

Thanks for your suggestion, I will use LTR_FINDER_parallel and LTRharvest_paralle

[oushujun]

Hello @oushujun @MoradMMokhtar , It is right that two different versions of genomes were wrong used. The reason for this problem is that the genome were splited single chrome sequence to run ltr_finder analysis parallelly to save running time. But I ignored combine the ltr_finder result with the input genome chromosome order. But in LTR_retriever analysis process, convert_ltr_finder.pl need the right order input ltr_finder combine result, otherwise it will result in " call_seq_by_list.pl line 129" error messages. In the original ltr_finder result have the cleary chromosome information,for example ">Sequence: Chr01 Len:111624253" in my ltr_finder result. It is better if convert_ltr_finder.pl could abstract the chromoseme id directly from original ltr_finder result.

Thanks

There's some good digging here. Yes, the convert_ltr_finder.pl script is based on the order of input sequence and it's not good for split genomes. A much faster way to acclerate large genomes is LTR_FINDER_parallel and LTRharvest_parallel. Thus this old way is not supported anymore and I decide not to fix it for the sake of time.

Best,
Shujun