laila...@aucegypt.edu
I hope everything is well at your end. I am new to deconseq, & I need to use it urgently to decontaminate sequences from metagenomic data coming from illumina sequences. I do have a reference E. coli genome downloaded from ncbi that I wish to decontaminate their sequences.
(First quickly, is there a way to do this on a windows pc?)
I'm now trying to install it on a Mac computer & I did the following:
Last login: Wed Feb 22 11:33:19 on console
AUCs-iMac-3:~ biolab$ cd Desktop/
AUCs-iMac-3:Desktop biolab$ cd deconseq-standalone-0.4.3
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ -man
-bash: -man: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ ls
COPYING README bwasw_modified_source
ChangeLog bwa64 deconseq.pl
DeconSeqConfig.pm bwaMAC splitFasta.pl
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ readme
-bash: readme: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ deconseq.pl
-bash: deconseq.pl: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 810
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwasw_modified_source/bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[2] 824
[1] Exit 127 bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwasw_modified_source/bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[3] 825
[2] Exit 126 bwasw_modified_source/bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ cd bwasw_modified_source/
[3]+ Exit 126 bwasw_modified_source/bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1 (wd: ~/Desktop/deconseq-standalone-0.4.3)
(wd now: ~/Desktop/deconseq-standalone-0.4.3/bwasw_modified_source)
AUCs-iMac-3:bwasw_modified_source biolab$ bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 860
AUCs-iMac-3:bwasw_modified_source biolab$ pwd
/Users/biolab/Desktop/deconseq-standalone-0.4.3/bwasw_modified_source
[1]+ Exit 127 bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:bwasw_modified_source biolab$ pwd \Desktop
/Users/biolab/Desktop/deconseq-standalone-0.4.3/bwasw_modified_source
AUCs-iMac-3:bwasw_modified_source biolab$ cd /Desktop
-bash: cd: /Desktop: No such file or directory
AUCs-iMac-3:bwasw_modified_source biolab$ cd /Users/biolab/Desktop/deconseq-standalone-0.4.3
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 880
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ -help bwaMAC
-bash: -help: command not found
[1]+ Exit 127 bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwaMAC -help
-bash: bwaMAC: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ -help bwaMAC
-bash: -help: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ -h bwaMAC
-bash: -h: command not found
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 887
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[2] 892
[1] Exit 127 bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[3] 903
[2] Exit 127 bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[4] 913
[3] Exit 126 ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ cd /Users/biolab/Desktop/
[4]+ Exit 126 ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1 (wd: ~/Desktop/deconseq-standalone-0.4.3)
(wd now: ~/Desktop)
AUCs-iMac-3:Desktop biolab$ cd /Users/biolab/Desktop
AUCs-iMac-3:Desktop biolab$ tar deconseq-standalone-0.4.3.tar
Usage:
List: tar -tf <archive-filename>
Extract: tar -xf <archive-filename>
Create: tar -cf <archive-filename> [filenames...]
Help: tar --help
AUCs-iMac-3:Desktop biolab$ tar -xf deconseq-standalone-0.4.3.tar
AUCs-iMac-3:Desktop biolab$ tar -zxvf deconseq-standalone-0.4.3.tar
x deconseq-standalone-0.4.3/
x deconseq-standalone-0.4.3/COPYING
x deconseq-standalone-0.4.3/deconseq.pl
x deconseq-standalone-0.4.3/bwasw_modified_source/
x deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2.h
x deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2_aux.c
x deconseq-standalone-0.4.3/bwasw_modified_source/bwtsw2_main.c
x deconseq-standalone-0.4.3/bwasw_modified_source/stdaln.c
x deconseq-standalone-0.4.3/bwasw_modified_source/bwaMAC
x deconseq-standalone-0.4.3/bwasw_modified_source/bwa64
x deconseq-standalone-0.4.3/bwasw_modified_source/stdaln.h
x deconseq-standalone-0.4.3/splitFasta.pl
x deconseq-standalone-0.4.3/DeconSeqConfig.pm
x deconseq-standalone-0.4.3/README
x deconseq-standalone-0.4.3/bwaMAC
x deconseq-standalone-0.4.3/ChangeLog
x deconseq-standalone-0.4.3/bwa64
AUCs-iMac-3:Desktop biolab$ ln -s deconseq-standalone-0.4.3 deconseq
AUCs-iMac-3:Desktop biolab$ cd deconseq
AUCs-iMac-3:deconseq biolab$ chmod +x *.pl
AUCs-iMac-3:deconseq biolab$ chmod +x bwa64
AUCs-iMac-3:deconseq biolab$ ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 938
AUCs-iMac-3:deconseq biolab$ bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[2] 944
[1] Exit 126 ./bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq biolab$ cd /Users/biolab/Desktop/
[2]+ Exit 127 bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1 (wd: ~/Desktop/deconseq)
(wd now: ~/Desktop)
AUCs-iMac-3:Desktop biolab$ cd /Users/biolab/Desktop
AUCs-iMac-3:Desktop biolab$ cd deconseq-standalone-0.4.3
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 950
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ chmod +x bwaMAC
[1]+ Exit 127 bwa64 index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna > out.txt 2>&1
AUCs-iMac-3:deconseq-standalone-0.4.3 biolab$ bwaMAC index -p ecoli -a bwtsw NC_010473_E.coli DH10B for removal.fna >out.txt 2>&1 &
[1] 961
I tried to download the human reference genome & do the following steps as in this page: http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/deconseq.htm, but the rest of the commands didn't work, it's saying 'wget command can not be found', but I have managed to download the commands & they are executable now. I'm working on a terminal, shall I be using something else? Should I use bwa64 or bwaMAC command?
I appreciate it if someone can help me with this, it would be great help.
Thank you,
Laila Ziko