I have been trying to use FUR to find unique genomic islands in a number of bacterial species, for example Strep Pyogenes. I am downloading the latest complete genomes from the relevant taxa id from NCBI for my target and similar for a close relative for my neighbourhood.

This produces output for some species- e.g. Rickettsia prowazekii, but only from the first step, i.e. using the -u flag. Even when I do get output it is usually very short sequences, and a very small amount of the genome.

According to the outputs of multiple alignments, and other techniques such as ANI analysis, there should be output for these species. For those species for which I do obtain some output, I would expect much more.

Is this an issue with the software or with the way I am running it? I.e. if I reduced the number of target genomes, would that help, and if so how should I select the ones to include? I really liked the paper and the algorithm so had high hopes for this software, but at present am not able to use it due to this issue.

Hi,

I am following the tutorial for real data, and at page 85, section 84c, I get the follow error while running fur -d eco105.db/ > eco105.fasta

fur - couldn't read the datatase version from  4.0

I am running the tutorial inside the provided docker container.

Any idea?
Thanks,
William

Hi @haubold .
I've been trying to use de docker image haubold/fox and I think I have a permission issue.
When running the container (docker run -it --detach-keys="ctrl-@" haubold/fox:latest) I can't access the files inside the path I'm in, even trying to mount (docker run --rm --user $(echo $UID):$(echo $UID) -it -v $(pwd):/data/ haubold/fox:latest).

But if run docker run --rm -it -v $(pwd):/app/ haubold/fox:latest ls -l /app I can see the directory content as below:

total 28
drwxr-xr-x 2 root root  4096 Aug 16 13:19 fur
drwxrwxr-x 2 jdoe jdoe 12288 Aug 16 14:39 neigbors_mplutonius
drwxrwxr-x 2 jdoe jdoe  4096 Aug 16 14:28 neigbors_plarvae
drwxrwxr-x 2 jdoe jdoe  4096 Aug 16 14:21 target_mplutonius
drwxrwxr-x 2 jdoe jdoe  4096 Aug 16 14:19 target_plarvae

How can I fix this permission issue, please?

Hi,

Thanks for developing this software, it looks really useful. I ran into an issue while running simple case of 1 target sequence and 29 neighbors. I noticed this was also reported in issue #2

After makeFurDb completed without error, I received the following while trying to run fur itself:

fur  -d database/
# Step                    Sequences  Nucleotides  Mutations (N)
# -------------------------------------------------------------
# Sliding window               1096       593912              0
error in fur: efopen, can't open database//p.fasta

I was able to replicate this issue using a small set of publicly available e coli genomes:
test.tar.gz

Thanks,

Joel

Hi,

Thanks for publishing this software. I encountered the problem of reading fasta file. The targets and neighbors are Salmonella enterica but differed from serovar. The sample are all from NCBI reference genome(like). When I try to run makeFurDb, it gives me error about reading FASTA file. Can you please help with this?

Thanks,
Ming

makeFurDb -t targets -n neighbors -d furDb
# Reading data...done.
' in sequence on line 4th target representative "targets/GCA_002048395.1_ASM204839v1_genomic.fna"...macle: <stdin>: Unexpected character '
Invalid FASTA file!

Thanks for making and sharing fur!

I am running into the issue #4 when trying to use fur for a single target from the docker image. I think the docker image has an older version before #4 was fixed. Would it be possible to update the docker?

Hello, thanks for making and sharing Fur!

Please could you help me with an error that occurs when I try to install fur?

I have installed make, gloang, noweb and git, and cloned fur (git clone https://github.com/EvolBioInf/fur.git). Then when I use the make command most of the packages are installed successfully but there is an error for makeFurDb: divsufsort64.h is not found.

Thanks for your help!

Rob

I expected to see a difference in results when adjusting the -p parameter, but this was not the case. I checked this by looking at the md5sum of the output fasta (where created, see other issue that I'm about to raise).

Hi author, I just download tutorial data and follow the exact step of document fur.pdf. When I run docker
sudo docker container run -v <Tutorial_data_place> --detach-keys="ctrl-@" -h fox -it haubold/fox
and run

fur -d furDb > tmpl.fasta
It presents the error message above
even when I type fur and enter it still errs like that

Hello, thanks for creating fur.

I have some trouble with the install of fur. When I use the make command, I get the following error:

make[1]: Entering directory '/mnt/c/Users/Paco/Desktop/fur/stream'
awk -f ../scripts/preTangle.awk stream.org | bash ../scripts/org2nw | notangle -Rstream.go | gofmt > stream.go
go build -ldflags "-X github.com/evolbioinf/fur/util.version=v4.2-11-g06c391e -X github.com/evolbioinf/fur/util.date=11_Feb_2024" stream.go
awk '$6==1' sim.dat | awk '{print $1, $2, $5}' > time_1.dat
plotLine -L -x "Sequence Length (Mb)" -y "Time (s)" -d "6cm,5cm" -p time_1.ps time_1.dat
/bin/sh: 1: plotLine: not found
make[1]: *** [Makefile:12: time_1.ps] Error 127
make[1]: Leaving directory '/mnt/c/Users/Paco/Desktop/fur/stream'

What can I do to fix this problem?

Thanks for helping me.

Paco

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 }'

Hi,

Thanks for developing this software.

I would like to ask how to select the neighbors genomes. Sometimes there are no sequences in the results of fur.

Thanks.

Is there a method of choosing the index target representative for the macle index when running makeFurDb?

Dear author,

When building the bin file "makeFurDB", there is an error "package github.com/evolbioinf/esa: build constraints exclude all Go files in /home/xiayao/tools/fur/makeFurDb/esa". I do not have root access. Is there anyway to solve this problem?

Thanks for your time.

Hi,

When there are a lot of contigs, makeFurDb is very slow.
The following figure shows the statistical results of the neighbor genomes.

Is there a way to increase speed? I am using the latest docker version.
Thanks.

Hi,

I think the output of fur2prim is inserting an "f" before PRIMER_MAX_TM. Is this correct or an error?

PRIMER_PRODUCT_SIZE_RANGE=70-150
PRIMER_MIN_TM=54.0
fPRIMER_MAX_TM=58.0
PRIMER_INTERNAL_MIN_TM=43.0
PRIMER INTERNAL_MAX_TM=47.0

i am facing this error while running fur, no clue where i did wrong.

Step Sequences Nucleotides Mutations (N)

-------------------------------------------------------------

Sliding window 0 0 0

error in fur: efopen, can't open /home/mrstrange/SSPD1/furDb/p.fasta.