Open ookil opened 5 years ago
cjw85
commented
5 years ago The screenshot indicates that cmake is not installed on your system. This is required to compile the third-party racon code. You should install this using your system package manager. We will update the README to make this clear. Sorry for the inconvenience.
ookil
commented
5 years ago Thank you. But I got another problem, hope it's okay to post it here
(pomoxis) umian@umach:~/pomoxis$ mini_assemble -i /media/umian/Toshiba/candida_pacbio.fasta -r /media/umian/Toshiba/candida_reference1.fasta -o /media/umian/Toshiba/Ref_nanopore -p ref_assembly Copying FASTA input to workspace: /media/umian/Toshiba/candida_pacbio.fasta > /media/umian/Toshiba/Ref_nanopore/ref_assembly.fasta Skipped adapter trimming. Skipped pre-assembly correction. Using supplied reference to perform reference-guided consensus. Running racon read shuffle 1... Running round 1 consensus... [M::mm_idx_gen::0.3780.80] collected minimizers [M::mm_idx_gen::0.5850.87] sorted minimizers [M::main::0.5850.87] loaded/built the index for 14 target sequence(s) [M::mm_mapopt_update::0.6130.88] mid_occ = 14 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 14 [M::mm_idx_stat::0.6380.88] distinct minimizers: 2204001 (96.66% are singletons); average occurrences: 1.048; average spacing: 5.343 [M::worker_pipeline::28.6740.31] mapped 19 sequences [M::main] Version: 2.10-r761 [M::main] CMD: minimap2 -t1 /media/umian/Toshiba/candida_reference1.fasta ref_assembly.fasta [M::main] Real time: 28.740 sec; CPU: 9.016 sec [racon::Polisher::initialize] loaded target sequences [bioparser::FastaParser] error: invalid file format!
Im not sure which file has invalid format. Both are in fasta which should be okay comparing with docs. But a little background:
1.Reference file was from NCBI so I changed it to fasta --> cp candida_reference.fna candida_reference.fasta (At first I put it in .fna format but got an error early on)
cat candida_reference.fasta | awk '{if (substr($0,1,1)==">"){if (p){print "\n";} print $0} else printf("%s",$0);p++;}END{print "\n"}' > candida_reference1.fasta as recommended on some forumWell in each case I recived the same error. Any idea what's wrong? Or should I seek help on racon sites?
I ran into some problems and not sure what to do now. I installed pomoxis how it's written in guide but I get an error with racon. I then activated venv and wanted to check if mini_assemble will work but it's not working.
Here's a screenshot.