dudcha
commented
1 year ago This suggests there is an inconsistency between your fasta file and the merged_nodups you are passing. Are you the merged_nodups was generated via alignment to this fasta? I suggest manually checking: go ahead and open the merged nodups file and look at the molecule names. DO they match those in the fasta? -Olga
xingguowu
When I run 3d-dna, the commands I run are as follows: bash run-asm-pipeline.sh -q 1 -r 0 --editor-repeat-coverage 50 -e /my_path/genome.fa /my_path/mergednodups.txt But the program did not generate hic file. Program error "temp. genome.0.asm mnd.txt does not exist or does not contain any reads." and stoped running
Starting iterating scaffolding with editing: ...starting round 0 of scaffolding: :) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true. :) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size :) -q flag was triggered, starting calculations with 1 threshold mapping quality ...Using cprops file: genome.0.cprops ...Using merged_nodups file: genome.mnd.0.txt ...Scaffolding all scaffolds and contigs greater or equal to 15000 bp. ...Starting iteration # 1 :) DONE! ...visualizing round 0 results: :) -p flag was triggered. Running with GNU Parallel support parameter set to true. :) -q flag was triggered, starting calculations for 1 threshold mapping quality :) -i flag was triggered, building mapq without :) -c flag was triggered, will remove temporary files after completion ...Remapping contact data from the original contig set to assembly ...Building track files ...Building the hic file temp.genome.0.asm_mnd.txt does not exist or does not contain any reads.