Open diego-rt opened 2 days ago
Hello,
I'm trying out Ribotin to assemble some tangles. They are probably not rRNA but I assume that it doesn't really matter. The morph size appears to be around 3 kbp.
ribotin-ref --approx-morphsize 3000 -r morphs.fa -i ../reads/hifi_reads.fastq.gz --nano ../reads/ont_reads.fastq.gz -o output_folder5 -t 16
However, I am getting the following error after clustering:
ribotin-ref version bioconda 1.3 checking for MBG /users/diego.terrones/miniforge3/envs/ribotin/bin/MBG checking for GraphAligner /users/diego.terrones/miniforge3/envs/ribotin/bin/GraphAligner using reference from morphs.fa output folder: output_folder5 extracting HiFi/duplex reads running running MBG MBG command: MBG -o output_folder5/graph.gfa -i output_folder5/hifi_reads.fa -k 101 -w 71 -a 2 -u 3 -r 600 -R 4000 --error-masking=msat --output-sequence-paths output_folder5/paths.gaf --only-local-resolve 1> output_folder5/mbg_stdout.txt 2> output_folder5/mbg_stderr.txt reading graph getting consensus consensus length 3212bp writing consensus reading read paths getting variants 147 variants writing variants writing variant graph writing allele graph writing variant vcf extracting ultralong ONT reads consensus length 3212, using 1606 as minimum ONT match length start ultralong ONT analysis aligning ultralong ONT reads to allele graph GraphAligner command: GraphAligner -g output_folder5/allele-graph.gfa -f output_folder5/ont_reads.fa -a output_folder5/ont-alns.gaf -t 16 --seeds-mxm-length 30 --seeds-mem-count 10000 --bandwidth 15 --multimap-score-fraction 0.99 --precise-clipping 0.85 --min-alignment-score 5000 --discard-cigar --clip-ambiguous-ends 100 --overlap-incompatible-cutoff 0.15 --mem-index-no-wavelet-tree --max-trace-count 5 1> output_folder5/graphaligner_stdout.txt 2> output_folder5/graphaligner_stderr.txt reading allele graph reading consensus extract corrected ultralong paths consensus path length 3212, using 1606 as minimum morph length 961 corrected paths extract loops from ONTs 15114 loops in ONTs cluster loops roughly max clustering edit distance 200 aligning morph path pair 0 / 114208941 aligning morph path pair 1000000 / 114208941 [...] aligning morph path pair 114000000 / 114208941 2 rough clusters cluster loops by density edit distance peak at 0 recluster with max edit distance 5, min points 5 cluster 0 with 8 reads reclustered to 1 clusters, sizes: 7 cluster 1 with 15106 reads reclustered to 14 clusters, sizes: 47 54 209 41 22 1230 536 78 18 11396 205 57 77 1130 15 density clusters phase clusters 15 phased clusters getting morph consensuses ribotin-ref: src/ClusterHandler.cpp:3137: std::vector<Node> getConsensusPath(const std::vector<OntLoop>&, const GfaGraph&): Assertion `coreNodes.size() >= 1' failed. Aborted
Many thanks in advance!
Hi, could you share the output data files output_folder5/hifi_reads.fa and output_folder5/ont_reads.fa
output_folder5/hifi_reads.fa
output_folder5/ont_reads.fa
Hello,
I'm trying out Ribotin to assemble some tangles. They are probably not rRNA but I assume that it doesn't really matter. The morph size appears to be around 3 kbp.
However, I am getting the following error after clustering:
Many thanks in advance!