liaochenlanruo / bttoxin_digger Goto Github PK

Hi
I sucessfully download BtToxin_Digger with bioconda. But, when I tested the installation following instructions, there is an error as below.

(toxin) nanopore@pc102-X399-AORUS-XTREME:~$ BtToxin_Digger --SeqPath ./ --SequenceType nucl --Scaf_suffix .fna
cd-hit not in $PATH and binary not specified use --cd-hit-bin
Usage:
General usage: pgcgap [Modules] [Options]

Show parameters for each module: pgcgap [Assemble|Annotate|ANI|AntiRes|CoreTree|MASH|OrthoF|Pan|pCOG|VAR|STREE|ACC]

Show examples of each module: pgcgap Examples

open OUT file faild
[--All][--Assemble][--Annotate][--CoreTree][--Pan][--OrthoF][--ANI][--MASH][--pCOG][--VAR][--AntiRes][--STREE][--ACC][--strain_num (INT)][Required by "All", "CoreTree", "Pan", "VAR" and "pCOG"][--ReadsPath (PATH)][Required by "All", "Assemble" and "VAR"][--scafPath (PATH)][Required by "All", "Assess", "Annotate", "MASH" and "AntiRes"][--AAsPath (PATH)][Required by "All", "CoreTree", "OrthoF" and "pCOG"][--reads1 (STRING)][Required by "All", "Assemble" and "VAR"][--reads2 (STRING)][Required by "All", "Assemble" and "VAR"][--Scaf_suffix (STRING)][--filter_length (INT)][Required][--codon (INT)][Required by "All", "Annotate", "CoreTree" and "Pan"][--suffix_len (INT)][Required by "All", "Assemble" and "VAR"](Strongly recommended)[--logs (STRING)][--fasttree][Can be used with "CoreTree", "Pan" and "OrthoF"][--bsnum (INT)][Required by "CoreTree", "Pan", "OrthoF", "STREE", and "VAR"][--fastboot (INT)][Required by "CoreTree", "Pan", "OrthoF", "STREE", and "VAR"][--threads (INT)][--platform (STRING)][Required][--assembler (STRING)][Required][--kmmer (INT)][Required][--genomeSize (STRING)][Required][--short1 (STRING)][Required][--short2 (STRING)][Required][--long (STRING)][Required][--hout (STRING)][Required][--genus (STRING)][--species (STRING)][--CDsPath (PATH)][Required][-c (FLOAT)][-n (INT)][-G (INT)][-t (INT)][-aL (FLOAT)][-aS (FLOAT)][-g (INT)][-d (INT)][--GffPath (PATH)][Required][--PanTree][--identi (INT)][--Sprogram (STRING)][--queryL (FILE)][Required][--refL (FILE)][Required][--refgbk (FILE)][Required]full path and namerecommended[--qualtype (STRING)][Required][--qual (INT)][--length (INT)][--mincov (INT)][--minfrac (FLOAT)][--minqual (INT)][--ram (INT)][--db (STRING)][Required][--identity (INT)][Required][--coverage (INT)][Required][--seqfile (STRING)][--seqtype (STRING)][--evalue (FLOAT)][Required][--id (INT)][Required][--query_cover (INT)][Required][--subject_cover (INT)][Required][--Assess (STRING)][--abyss-bin (PATH)][--canu-bin (PATH)][--prodigal-bin (PATH)][--prokka-bin (PATH)][--cd-hit-bin (PATH)][--mafft-bin (PATH)][--pal2nal-bin (PATH)][--snp-sites-bin (PATH)][--roary-bin (PATH)][--orthofinder-bin (PATH)][--fastANI-bin (PATH)][--snippy-bin (PATH)][--sickle-bin (PATH)][--mash-bin (PATH)][--abricate-bin (PATH)][--unicycler-bin (PATH)][--muscle-bin (PATH)][--trimAL-bin (PATH)][--iqtree-bin (PATH)]The above document had some coding errors, which are explained below:

I hope someone can help me about this error. Thank you.

HI,
I have successfully installed and used BtToxin_Digger before but now I have a new server and installation in this one is becoming a tedious process. First I tried to install with Bioconda as I have done before. This time the process was taking forever to run and at the end conda couldn't find the package.
Then I thought of compiling it from source and after installing the dependencies and cloning the git hub repositories I tried the test command which gave me the following error:

Can't exec "pgcgap": No such file or directory at ../BtToxin_Digger line 311.
Can't exec "get_all_info_nucl.pl": No such file or directory at ../BtToxin_Digger line 319.
Can't exec "get_genes_table.pl": No such file or directory at ../BtToxin_Digger line 418.

I followed the instruction manual thoroughly. Hope someone could help me with this.