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UCSC-LoweLab / tRNAscan-SE

A program for detection of tRNA genes
GNU General Public License v3.0
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error：substr outside of string at tRNAscan-SE/tRNAscanSE/Utils.pm line 117, <__ANONIO__> line 16009. #16

Closed yweii closed 1 year ago

yweii commented 1 year ago

hi， I'm having trouble using tRNAscan-SE. input: tRNAscan-SE -B -o tRNA.out -f tRNA.ss -m tRNA.stats 001.fasta error: tRNAscan-SE v.2.0.9 (July 2021) - scan sequences for transfer RNAs Copyright (C) 2020 Patricia Chan and Todd Lowe University of California Santa Cruz Freely distributed under the GNU General Public License (GPLv3)

Sequence file(s) to search: 001.fasta Search Mode: Bacterial Results written to: tRNA.out Output format: Tabular Searching with: Infernal First Pass->Infernal Isotype-specific model scan: Yes Covariance model: /public/home/wyang/miniconda3/envs/trna/lib/tRNAscan-SE/models/TRNAinf-bact.cm /public/home/wyang/miniconda3/envs/trna/lib/tRNAscan-SE/models/TRNAinf-bact-SeC.cm Infernal first pass cutoff score: 10

Temporary directory: /tmp tRNA secondary structure predictions saved to: tRNA.ss Search statistics saved in: tRNA.stats Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan substr outside of string at /public/home/wyang/miniconda3/envs/trna/lib/tRNAscan-SE/tRNAscanSE/Utils.pm line 117, line 16009.

How to solve it?

THANKS！

yweii commented 1 year ago

hi， I think I have solved it, the reason is the format of the input file.