I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using:
./configure make make install
When I type
tRNAscan-SE --help, I get the help page:
tRNAscan-SE 2.0 (December 2017) FATAL: No sequence file(s) specified. Usage: tRNAscan-SE [-options] <FASTA file(s)> Scan a sequence file for tRNAs -- default: use Infernal & tRNA covariance models with eukaryotic sequences (use -B, -A, -M, -O or -G to scan other types of sequences) Basic Options -E : search for eukaryotic tRNAs (default) -B : search for bacterial tRNAs -A : search for archaeal tRNAs -M <model> : search for mitochondrial tRNAs options: mammal, vert -O : search for other organellar tRNAs -G : use general tRNA model (cytoslic tRNAs from all 3 domains included) -L : search using the legacy method (tRNAscan, EufindtRNA, and COVE) use with -E, -B, -A, -O, or -G -I : search using Infernal (default) use with -E, -B, -A, -O, or -G -o <file> : save final results in <file> -f <file> : save tRNA secondary structures to <file> -m <file> : save statistics summary for run in <file> (speed, # tRNAs found in each part of search, etc) -H : show both primary and secondary structure components to covariance model bit scores -q : quiet mode (credits & run option selections suppressed) -h : print full list (long) of available options
I then tried to use it with
tRNAscan-SE c_elegans.PRJNA13758.WS263.genomic.fa but it gave the following error:
FATAL: Unable to find /usr/local/bin/cmsearch executable
After googling cmsearch, it seems that is is part of the Infernal package. So, I installed infernal with conda using
conda install infernal.
I pulled the help from
cmsearch -h # cmsearch :: search CM(s) against a sequence database # INFERNAL 1.1.2 (July 2016) # Copyright (C) 2016 Howard Hughes Medical Institute. # Freely distributed under a BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Usage: cmsearch [options] <cmfile> <seqdb> Basic options: -h : show brief help on version and usage -g : configure CM for glocal alignment [default: local] -Z <x> : set search space size in *Mb* to <x> for E-value calculations (x>0) --devhelp : show list of otherwise hidden developer/expert options Options directing output: -o <f> : direct output to file <f>, not stdout -A <f> : save multiple alignment of all significant hits to file <s> --tblout <f> : save parseable table of hits to file <s> --acc : prefer accessions over names in output --noali : don't output alignments, so output is smaller --notextw : unlimit ASCII text output line width --textw <n> : set max width of ASCII text output lines  (n>=120) --verbose : report extra information; mainly useful for debugging Options controlling reporting thresholds: -E <x> : report sequences <= this E-value threshold in output [10.0] (x>0) -T <x> : report sequences >= this score threshold in output Options controlling inclusion (significance) thresholds: --incE <x> : consider sequences <= this E-value threshold as significant [0.01] --incT <x> : consider sequences >= this score threshold as significant Options controlling model-specific reporting thresholds: --cut_ga : use CM's GA gathering cutoffs as reporting thresholds --cut_nc : use CM's NC noise cutoffs as reporting thresholds --cut_tc : use CM's TC trusted cutoffs as reporting thresholds Options controlling acceleration heuristics*: --max : turn all heuristic filters off (slow) --nohmm : skip all HMM filter stages, use only CM (slow) --mid : skip first two HMM filter stages (SSV & Vit) --default : default: run search space size-dependent pipeline [default] --rfam : set heuristic filters at Rfam-level (fast) --hmmonly : use HMM only, don't use a CM at all --FZ <x> : set filters to defaults used for a search space of size <x> Mb --Fmid <x> : with --mid, set P-value threshold for HMM stages to <x> [0.02] Other options*: --notrunc : do not allow truncated hits at sequence termini --anytrunc : allow full and truncated hits anywhere within sequences --nonull3 : turn off the NULL3 post hoc additional null model --mxsize <x> : set max allowed alnment mx size to <x> Mb [df: autodetermined] --smxsize <x> : set max allowed size of search DP matrices to <x> Mb [128.] --cyk : use scanning CM CYK algorithm, not Inside in final stage --acyk : align hits with CYK, not optimal accuracy --wcx <x> : set W (expected max hit len) as <x> * cm->clen (model len) --toponly : only search the top strand --bottomonly : only search the bottom strand --tformat <s> : assert target <seqdb> is in format <s>: no autodetection --cpu <n> : number of parallel CPU workers to use for multithreads *Use --devhelp to show additional expert options.
I tried the tRNAscan-SE command again but it failed with the same error message.
So, tRNAscan-SE is looking for cmsearch in the wrong place. How can I make tRNAscan-SE use cmsearch successfully?
Forgot to tell you I am working on Mac OS X and that cmsearch is installed here:
python3env anaconda environment is active.