search

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
188 stars 40 forks source link

Errors in running LTR.identifier.pl #26

Closed caixu0518 closed 5 years ago

caixu0518 commented 5 years ago

Hi Shujun,

I encountered the following problem when running LTR_retriever. I don't know if these errors affect the results, or how I should fix them.

Tue Nov 13 22:48:20 CST 2018 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.

substr outside of string at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin### /LTR.identifier.pl line 317. Use of uninitialized value $seed in index at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 321. substr outside of string at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 317. Use of uninitialized value $seed in index at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 321. Use of uninitialized value $probTSD in uc at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 325. substr outside of string at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 317. Use of uninitialized value $seed in index at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 321. Use of uninitialized value $probTSD in uc at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 325. Use of uninitialized value $TSDlen in numeric le (<=) at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 334. Use of uninitialized value $probTSD in uc at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 334. Use of uninitialized value $probTSD in index at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 358. Use of uninitialized value $TSDlen in addition (+) at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 358. Use of uninitialized value $probTSD in index at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 359. Use of uninitialized value $TSDlen in numeric lt (<) at /disk02/caix/src/LTR_retriever/LTR_retriever-1.9/bin/LTR.identifier.pl line 360. Wed Nov 14 00:25:57 CST 2018 Intact LTR-RT found: 5490

Wed Nov 14 00:35:14 CST 2018 Module 6: Start to analyze truncated LTR-RTs... Truncated LTR-RTs without the intact version will be retained in the LTR-RT library. Use -notrunc if you don't want to keep them.

best, Xu Cai

oushujun commented 5 years ago

Hi Xu Cai,

If you only received a couple of such errors and the program produces intact LTR-RTs, as indicated in your standard output, you should be fine. This is likely the case that a small number of candidates are located at the boundary of contigs, such that no flanking sequence is available for the extraction. Missing these candidates will not produce significant bias. I will further work on a solution for this.

Thanks, Shujun

caixu0518 commented 5 years ago

Many thanks.