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I am getting following error while using hunt command:
"FM-Index cannot be loaded!"

The last release (0.1.7) was from last year, and there have been a few commits since. Should that binary release continue to be used?

I am unable to compile dicey on a Mac (MacBook Pro, M1 Max chip, 32 GB RAM, Ventura 13.4).

I have installed it using Biocanda in a conda environment. When trying to compile it I run into the following issue:

(probe_dicey) boehm0002@bz-rgmr01-plm02 dicey % make all
if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && /Library/Developer/CommandLineTools/usr/bin/make && /Library/Developer/CommandLineTools/usr/bin/make lib-static && cd ../../ && touch .htslib; fi
Can't exec "aclocal": No such file or directory at /opt/homebrew/Cellar/autoconf/2.71/share/autoconf/Autom4te/FileUtils.pm line 274.
autoreconf: error: aclocal failed with exit status: 2
make: *** [.htslib] Error 2

I was able to figure out that I should install automake as this contains aclocal, but I have a University managed computer and using brew to do this does not work well. Even after installation in admin mode I get the same message.

I then also tried to run dicey using docker afterwards and I run into the following issue when pulling it (I used Docker Desktop):
no matching manifest for linux/arm64/v8 in the manifest list entries

After some digging in stack-overflow I found that this is due to an issue with M1 chips and after resolving that I still received the same error as above. I am now stuck and unable to track down if this is actually a Mac issue or something else.

Many thanks for your help!!

Hi there,

Any idea how long Dicey takes to process a human reference genome with the chop function? My Macbook Pro has been running for 30 hours straight. Also, what size can I expect for the read1 and read2 files?

Thanks a million.

Niel

Hi,

I want to perform multiple in silico PCR's using Dicey. But every time I start a new search it seems like it has to load the full reference genome. Is there a more efficient way to load the reference genome only once and perform multiple searches against that reference genome?

Thanks!
Dion

Hello! I'm interested in generating a mappability map for a genome for Delly germinal CNV calling. There are several arguments for dicey chop including insert size, read length etc. Would I need to set those arguments to whatever match the reads that I'll be using or should they just remind default? Thank you so much for your time.

I am trying to understand how to adjust -k since it seems to impact the results dramatically.
For example with primers of length 25 and a -k of 15 I get no amplicons.
I think this is the same as changing the Number of bp from the 3' End of the Primer Used to Seach for Matches (>14) param on the Silica website.
https://www.gear-genomics.com/silica/index.html?UUID=0101f455-249c-4e7f-beb5-63f2f50a7501

If I change this to -k 20 or the same param on the website I get an amplicon
https://www.gear-genomics.com/silica/index.html?UUID=c40f28ba-5abd-420a-8d45-6667d72de0fe

I'm trying to dicey index a 2.4Gb plant genome assembly. How long should I expect creating the FM-Index to take, roughly?

I have an error when I run dicey..
my commands are:

script="/media/bioadmin/24e12c01-7941-49f5-9647-eeebabd15082/packages/dicey/scripts/json2txt.py"
config="/media/bioadmin/24e12c01-7941-49f5-9647-eeebabd15082/packages/dicey/src/primer3_config"

echo -e ">566F\CAGCAGCCGCGGTAATTCC\n>1200R\nCCCGTGTTGAGTCAAATTAAGC" > primers.fa

dicey search -c 45 -l 1000 -g ../18S_All.fasta primers.fa -i $config | python $script

I get the error:

Error opening params file
Error opening params file
Segmentation fault (core dumped)

Dicey could support symlinks for some regular inputs instead of just regular files. For example, this would allow a symlinked assembly or indices for that assembly to be used for dicey search, and also process substitution could be used to send the input sequences fasta from standard input or the output of another application:

dicey search  -i /etc/primer3_config -g symlink.fa.gz <(echo "FASTA here)

Relevant lines:
https://github.com/gear-genomics/dicey/blob/main/src/silica.h#L300
https://github.com/gear-genomics/dicey/blob/main/src/silica.h#L363

I got an error with "FM-Index cannot be loaded!"

Here is my command

dicey search -c 45 -g Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz primers.fa -i /dicey/src/primer3_config/

I am not familar with C++, but i search for the error for a long time and i think there is somthing wrong with the genomeindex.json
file. But I have load all the reference file from the recommend webset as following: fa.gz file, fa.gz.fai file, fa.gz.gzi file and the fa.fm9 file.

I really struggled with the error for many days, so it will be very appriciate for any advise!

Thank a ton!

Hello! Thanks for this great tool.

I'm using dicey hunt to check for uniqueness of primers in my target genome, and would like to do it in routine on a set of sequences, instead of one by one - could you/we add this as an input CLI parameter?

Best,
Brice