TEstrainer error - Githubissues

Hi, thanks for providing this helpful pipeline! I installed earlgrey3.2 with conda. My run died at the TEstrainer step with the following error message:

<<< Straining TEs and Refining de novo Consensus Sequences >>>

Splitting run 1 Initial trf check for 1 Initial blast and preparation for MSA 1 Primary alignment run 1 Trimming run 1 Finished extension cat: 'TS_mAcoRus-families.fa2547/run*/complete_mAcoRus-families.fa': No such file or directory Splitting for simple/satellite packages Running TRF Running SA-SSR

Finding SSRs: Running mreps Trimming and sorting based on mreps, TRF, SA-SSR Error in dplyr::mutate(): ℹ In argument: period = as.double(width(ssr)). Caused by error: ! unable to find an inherited method for function ‘width’ for signature ‘"logical"’ Backtrace: ▆

├─... %>% filter(count > 2)
├─dplyr::filter(., count > 2)
├─dplyr::arrange(., seqnames)
├─dplyr::inner_join(., in_seq_tbl, by = "seqnames")
├─dplyr::mutate(., draft_seqnames = sub("#.*", "", seqnames))
├─dplyr::mutate(...)
├─dplyr::mutate(., ssr = ifelse(is.na(ssr), "NA", ssr), period = as.double(width(ssr)))
├─dplyr:::mutate.data.frame(., ssr = ifelse(is.na(ssr), "NA", ssr), period = as.double(width(ssr)))
│ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
1. │ ├─base::withCallingHandlers(...)
2. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
3. │ └─mask$eval_all_mutate(quo)
4. │ └─dplyr (local) eval()
5. ├─BiocGenerics::width(ssr)
6. │ └─methods (local) <fn>(<list>, <stndrdGn>, <env>)
7. │ └─base::stop(...)
8. └─base::.handleSimpleError(...)
9. └─dplyr (local) h(simpleError(msg, call))
10. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Removing temporary files Reclassifying repeats cp: cannot stat 'TS_mAcoRus-families.fa_2547/trf/mAcoRus-families.fa.nonsatellite': No such file or directory No database indicated or it is an empty file.

/home/huayun/mdwilson/huayun/miniconda3/envs/earlgrey/bin/RepeatClassifier - 2.0.5 NAME RepeatClassifier - Classify Repeat Models

SYNOPSIS RepeatClassifier [-options] -consensi [-stockholm ]

DESCRIPTION The options are:

-h(elp)
    Detailed help

CONFIGURATION OVERRIDES -ninja_dir The path to the installation of the Ninja phylogenetic analysis package.

-ucsctools_dir <string>
    The path to the installation directory of the UCSC TwoBit Tools
    (twoBitToFa, faToTwoBit, twoBitInfo etc).

-repeatmasker_dir <string>
    The path to the installation of RepeatMasker (RM 4.1.4 or higher)

-trf_dir <string>
    The full path to TRF program. TRF must be named "trf". ( 4.0.9 or
    higher )

-cdhit_dir <string>
    The path to the installation of the CD-Hit sequence clustering
    package.

-rmblast_dir <string>
    The path to the installation of the RMBLAST (2.13.0 or higher)

-recon_dir <string>
    The path to the installation of the RECON de-novo repeatfinding
    program.

-genometools_dir <string>
    The path to the installation of the GenomeTools package.

-ltr_retriever_dir <string>
    The path to the installation of the LTR_Retriever (v2.9.0 and
    higher) structural LTR analysis package.

-rscout_dir <string>
    The path to the installation of the RepeatScout ( 1.0.6 or higher )
    de-novo repeatfinding program.

-mafft_dir <string>
    The path to the installation of the MAFFT multiple alignment
    program.

TobyBaril / EarlGrey

TEstrainer error #64