Test data

[ValentinaPeona]

Thanks for developing MicroFinder!

I am trying to run MicroFinder on the test data, however I am not sure I am getting the expected output because some files are empty.

I created the Singularity image

singularity pull --disable-cache docker://ghcr.io/sanger-tol/microfinder:main

then I ran it on the test data:

singularity run -B $PWD --pwd $PWD microfinder_main.sif $PWD/test/test.fa 5000000

[M::mp_ntseq_read@0.001*2.15] read 22 bases in 5 contigs
[M::mp_idx_build@0.001*2.12] 10 blocks
[M::mp_idx_build@0.003*1.26] collected syncmers
[M::mp_idx_build@0.108*0.56] 0 kmer-block pairs
[M::mp_idx_print_stat] 0 distinct k-mers; mean occ of infrequent k-mers: -nan; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::0.490*0.52] mapped 2882 sequences
[M::main] Version: 0.14-r265
[M::main] CMD: miniprot --gff /cluster/home/pvalentina/scratch/Tools/MicroFinder/test/test.fa /usr/src/app/data/MicroFinder_prot_set.v0.1.fa.gz
[M::main] Real time: 0.500 sec; CPU: 0.264 sec; Peak RSS: 0.074 GB

ll test
total 9
-rw-r--r-- 1 pvalentina pvalentina-group 42 Oct  1 10:25 test.fa
-rw-r--r-- 1 pvalentina pvalentina-group 16 Oct  1 12:55 test.fa.MicroFinder.gff
-rw-r--r-- 1 pvalentina pvalentina-group 42 Oct  1 12:55 test.fa.MicroFinder.ordered.fa
-rw-r--r-- 1 pvalentina pvalentina-group  0 Oct  1 12:55 test.fa.MicroFinder.order.tsv
-rw-r--r-- 1 pvalentina pvalentina-group 16 Oct  1 10:25 test.order

The output gff is basically empty, but I guess it's okay because it's just very short sequences. The ordered.fa has indeed a different order with respect to test.fa

cat test/test.order 
a	2
b	1
c	1
e	4

cat test/test.fa
>a
acgtn
>b
CGTN
>c
CGTNA
>d
CGGGGG
>e
AC

Is that what it is supposed to look like?

But I also wanted to test it with the data suggested in the README but that gave me this error. Is it possible to get this data as test?

singularity run --disable-cache -B `pwd`:/data docker://ghcr.io/sanger-tol/microfinder:main /data/bLarArg3.1.HAP1.primary.curated.fa 5000000
INFO:    Downloading library image to tmp cache: /tmp/sbuild-tmp-cache-660255487
INFO:    Converting OCI blobs to SIF format
WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process
INFO:    Starting build...
INFO:    Fetching OCI image...
61.4MiB / 61.4MiB [======================================================================================================] 100 % 25.8 MiB/s 0s
39.5MiB / 39.5MiB [======================================================================================================] 100 % 25.8 MiB/s 0s
1.0MiB / 1.0MiB [========================================================================================================] 100 % 25.8 MiB/s 0s
4.6MiB / 4.6MiB [========================================================================================================] 100 % 25.8 MiB/s 0s
47.3MiB / 47.3MiB [======================================================================================================] 100 % 25.8 MiB/s 0s
22.9MiB / 22.9MiB [======================================================================================================] 100 % 25.8 MiB/s 0s
201.6MiB / 201.6MiB [====================================================================================================] 100 % 25.8 MiB/s 0s
9.5MiB / 9.5MiB [========================================================================================================] 100 % 25.8 MiB/s 0s
INFO:    Extracting OCI image...
INFO:    Inserting Apptainer configuration...
INFO:    Creating SIF file...
[===================================================================================================================================] 100 % 0s
[ERROR] failed to open/build the index
/usr/local/bundle/gems/bio-2.0.6/lib/bio/io/flatfile/buffer.rb:57:in 'File#initialize': No such file or directory @ rb_sysopen - /data/bLarArg3.1.HAP1.primary.curated.fa (Errno::ENOENT)
	from /usr/local/bundle/gems/bio-2.0.6/lib/bio/io/flatfile/buffer.rb:57:in 'IO.open'
	from /usr/local/bundle/gems/bio-2.0.6/lib/bio/io/flatfile/buffer.rb:57:in 'Bio::FlatFile::BufferedInputStream.open_file'
	from /usr/local/bundle/gems/bio-2.0.6/lib/bio/io/flatfile.rb:157:in 'Bio::FlatFile._open_file'
	from /usr/local/bundle/gems/bio-2.0.6/lib/bio/io/flatfile.rb:105:in 'Bio::FlatFile.open'
	from /usr/src/app/sort_fasta.rb:38:in '<main>'

Thanks for your help!

[epaule]

a.) the test.fa look fine. It will be just sorted by size, as it will not have any miniprot hits.
b.) we haven't included the bLarArg3 fasta, but you can get a version from: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_964417175.1/