Macle.idx is not accessible.

[KarthikStrange]

Macle.idx is not accessible.

i did export bashrc

export PATH=$PATH:/home/mrstrange/macle

./fur -d /home/mrstrange/SSPD/furDb/ ERROR: Could not open file: /home/mrstrange/SSPD/furDb//macle.idx open(/home/mrstrange/SSPD/furDb//macle.idx, 0) failed: No such file or directory error in fur: couldn't run macle -l /home/mrstrange/SSPD/furDb//macle.idx | head -n 6 | tail -n 1 | awk '{print $6 }'

[haubold]

It looks as if makeFurDb ended wihout generating the file macle.idx. What happens when you run makeFurDb on your targets and neighbors?

[KarthikStrange]

makeFurDb -t /home/mrstrange/SSPD/target/ -n /home/mrstrange/SSPD/neighborhood/ -d furDb

Reading data...done.

Making macle index with target representative "/home/mrstrange/SSPD/target/*.fasta"...done.

Making BLAST database...sh: 1: makeblastdb: not found

it did generate macle.idx. but failed to run makeblastdb i tried searching whereis makeblastdb, it wasn't included in either macle/phlyonium/fur. not mentioned in dependency either.

is makeblastdb a seperate tool that macle / fur rely on? if that so,

https://github.com/JRymut/makeblastdb is this that git repository for it?

[haubold]

Glad to hear that macle.idx was constructed. As to makeblastdb, it is part of the ncbi-blast+ package, which is one of the dependencies of fur. The README of fur should contain the full list of dependencies (and does list ncbi-blast+, I just checked).

[KarthikStrange]

i installed ncbi-blast+ and it worked, Thank you so much sir. ./makeFurDb -t /home/mrstrange/SSPD/target/ -n /home/mrstrange/SSPD/neighborhood/ -d /home/mrstrange/SSPD/furDb/

Reading data...done.

Making macle index with target representative "/home/mrstrange/SSPD/target/*.fasta" ...done.

Making BLAST database...done.