substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129

[aaannaw]

Hello,
I am running LTR retriever, and I am coming across these errors:
/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.scn LTRretriever.genome.fna -f -g -max_ratio 50 /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.full -C LTRretriever.genome.fna substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129. .... /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -trf_path /data/00/user/user105/software/trf/trf -misschar N -nc 10 -nr 0.8 -minlen 100 -minscore 1000 -f LTRretriever.genome.fna.ltrTE.faIllegal division by zero at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl line 80, <File> chunk 10774. /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.scn LTRretriever.genome.fna.ltrTE.stg1 -x /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.extend -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.scn.adj LTRretriever.genome.fna.ltrTE.pass.list -i -N /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.adj.list -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.scn.adj LTRretriever.genome.fna.ltrTE.trunc.list -i -N -L /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.adj.list -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.ltrTE.veryfalse -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -nr 0.8 -minlen 100 -trf -trf_path /data/00/user/user105/software/trf/trf -cleanN -f LTRretriever.genome.fna.ltrTE.trunc.masked/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.all.scn LTRretriever.genome.fna.nmtf.pass.list -i -N /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -nr 0.8 -minlen 100 -trf -trf_path /data/00/user/user105/software/trf/trf -cleanN -f LTRretriever.genome.fna.prelib.INT.masked/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.out.LAI.LTRlist -C LTRretriever.genome.fna.

The stdout file is:
`Parameters: -genome LTRretriever.genome.fna -intact LTRretriever.genome.fna.pass.list -all LTRretriever.genome.fna.out -t 30 -q -blast /data/00/s
oftware/blast/ncbi-blast-2.10.0+/bin/

Mon Sep 16 06:40:30 CST 2024 Dependency checking: Passed!
Mon Sep 16 06:40:30 CST 2024 Calculation of LAI will be based on the whole genome.
Please use the -mono parameter if your genome is a recent ployploid, for high identity between homeologues will overcorrect raw LAI scores.
Mon Sep 16 06:40:30 CST 2024 Estimate the identity of LTR sequences in the genome: quick mode
Mon Sep 16 06:41:04 CST 2024 The identity of LTR sequences: 95.5290182971457%
Mon Sep 16 06:41:04 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 (0.45%) is too low for accurate LAI calculation (min 5% required)

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

Mon Sep 16 06:42:34 CST 2024 All analyses were finished!
##############################
####### Result files #########
##############################

Table output for intact LTR-RTs (detailed info)
LTRretriever.genome.fna.pass.list (All LTR-RTs)
LTRretriever.genome.fna.nmtf.pass.list (Non-TGCA LTR-RTs)
LTRretriever.genome.fna.pass.list.gff3 (GFF3 format for intact LTR-RTs)

LTR-RT library
LTRretriever.genome.fna.LTRlib.redundant.fa (All LTR-RTs with redundancy)
LTRretriever.genome.fna.LTRlib.fa (All non-redundant LTR-RTs)
LTRretriever.genome.fna.nmtf.LTRlib.fa (Non-TGCA LTR-RTs)

Whole-genome LTR-RT annotation by the non-redundant library
LTRretriever.genome.fna.out.gff (GFF format)
LTRretriever.genome.fna.out.fam.size.list (LTR family summary)
LTRretriever.genome.fna.out.superfam.size.list (LTR superfamily summary)`

The result LTRretriever.genome.fna.mod.LTRlib.redundant.fa file is missing.

Maybe the id of genome is too long? The input file LTRretriever.merged.scn is:

Could you give me any suggestions?
Looking forward with your reply.
Best wishes!
Na Wan

[oushujun]

You likely have input files do not match the genome version. Please double check Shujun

…

On Sun, Sep 15, 2024 at 10:33 PM aaannaw ***@***.***> wrote: Hello, I am running LTR retriever, and I am coming across these errors: /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ get_range.pl 1 LTRretriever.genome.fna.retriever.scn LTRretriever.genome.fna -f -g -max_ratio 50 /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.full -C LTRretriever.genome.fna substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl line 129. substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl line 129. .... /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -trf_path /data/00/user/user105/software/trf/trf -misschar N -nc 10 -nr 0.8 -minlen 100 -minscore 1000 -f LTRretriever.genome.fna.ltrTE.faIllegal division by zero at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl line 80, <File> chunk 10774. /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ get_range.pl 1 LTRretriever.genome.fna.retriever.scn LTRretriever.genome.fna.ltrTE.stg1 -x /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.extend -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ get_range.pl 1 LTRretriever.genome.fna.retriever.scn.adj LTRretriever.genome.fna.ltrTE.pass.list -i -N /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.adj.list -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ get_range.pl 1 LTRretriever.genome.fna.retriever.scn.adj LTRretriever.genome.fna.ltrTE.trunc.list -i -N -L /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.adj.list -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.ltrTE.veryfalse -C LTRretriever.genome.fna /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -nr 0.8 -minlen 100 -trf -trf_path /data/00/user/user105/software/trf/trf -cleanN -f LTRretriever.genome.fna.ltrTE.trunc.masked/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ get_range.pl 1 LTRretriever.genome.fna.retriever.all.scn LTRretriever.genome.fna.nmtf.pass.list -i -N /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/cleanup.pl -nr 0.8 -minlen 100 -trf -trf_path /data/00/user/user105/software/trf/trf -cleanN -f LTRretriever.genome.fna.prelib.INT.masked/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/ call_seq_by_list.pl LTRretriever.genome.fna.out.LAI.LTRlist -C LTRretriever.genome.fna. The stdout file is: `Parameters: -genome LTRretriever.genome.fna -intact LTRretriever.genome.fna.pass.list -all LTRretriever.genome.fna.out -t 30 -q -blast /data/00/s oftware/blast/ncbi-blast-2.10.0+/bin/ Mon Sep 16 06:40:30 CST 2024 Dependency checking: Passed! Mon Sep 16 06:40:30 CST 2024 Calculation of LAI will be based on the whole genome. Please use the -mono parameter if your genome is a recent ployploid, for high identity between homeologues will overcorrect raw LAI scores. Mon Sep 16 06:40:30 CST 2024 Estimate the identity of LTR sequences in the genome: quick mode Mon Sep 16 06:41:04 CST 2024 The identity of LTR sequences: 95.5290182971457% Mon Sep 16 06:41:04 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 (0.45%) is too low for accurate LAI calculation (min 5% required) Sorry, LAI is not applicable on the current genome assembly. Mon Sep 16 06:42:34 CST 2024 All analyses were finished! ############################## ####### Result files ######### ############################## Table output for intact LTR-RTs (detailed info) LTRretriever.genome.fna.pass.list (All LTR-RTs) LTRretriever.genome.fna.nmtf.pass.list (Non-TGCA LTR-RTs) LTRretriever.genome.fna.pass.list.gff3 (GFF3 format for intact LTR-RTs) LTR-RT library LTRretriever.genome.fna.LTRlib.redundant.fa (All LTR-RTs with redundancy) LTRretriever.genome.fna.LTRlib.fa (All non-redundant LTR-RTs) LTRretriever.genome.fna.nmtf.LTRlib.fa (Non-TGCA LTR-RTs) Whole-genome LTR-RT annotation by the non-redundant library LTRretriever.genome.fna.out.gff (GFF format) LTRretriever.genome.fna.out.fam.size.list (LTR family summary) LTRretriever.genome.fna.out.superfam.size.list (LTR superfamily summary)` The result LTRretriever.genome.fna.mod.LTRlib.redundant.fa file is missing. image.png (view on web) <https://github.com/user-attachments/assets/76f907e2-ebb3-4162-98fe-799f5d51108e> Maybe the id of genome is too long? The input file LTRretriever.merged.scn is: image.png (view on web) <https://github.com/user-attachments/assets/ad4d4625-2b85-4a81-ad78-1ca3f0ba18b8> Could you give me any suggestions? Looking forward with your reply. Best wishes! Na Wan — Reply to this email directly, view it on GitHub <#178>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NAVXZNM2QL2RUZ7WYLZWY7OBAVCNFSM6AAAAABOIMSSV2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDOMZYGM4DSNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>