hej :)
I tried to run only that step:
sh ../software/3d-dna-master/visualize/run-assembly-visualizer.sh -p false juicebox/pin_HiC_run"$run".assembly juicebox/Charengus_HiCPacBio_sorted_dedup_filter.sorted.links.mnd
but unfortunately got:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
...Remapping contact data from the original contig set to assembly
../software/3d-dna-master/visualize/run-assembly-visualizer.sh: eval: line 161: syntax error near unexpected token (' ../software/3d-dna-master/visualize/run-assembly-visualizer.sh: eval: line 161: awk -v scale=1 -f /proj/snic2021-2-4/private/herring/users/sabine/software/3d-dna-master/lift/lift-input-mnd-to-asm-mnd.awk <(awk '$0~/^>/{$1=substr($1,2); print}' juicebox/pin_HiC_run3.assembly) <(awk '$0!~/^>/' juicebox/pin_HiC_run3.assembly) juicebox/Charengus_HiCPacBio_sorted_dedup_filter.sorted.links.mnd > temp.pin_HiC_run3.asm_mnd.txt'
I hope you can please help out.
thanks a lot,
myo
hej :)
I tried to run only that step:
sh ../software/3d-dna-master/visualize/run-assembly-visualizer.sh -p false juicebox/pin_HiC_run"$run".assembly juicebox/Charengus_HiCPacBio_sorted_dedup_filter.sorted.links.mnd
but unfortunately got:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
...Remapping contact data from the original contig set to assembly
../software/3d-dna-master/visualize/run-assembly-visualizer.sh: eval: line 161: syntax error near unexpected token
(' ../software/3d-dna-master/visualize/run-assembly-visualizer.sh: eval: line 161:awk -v scale=1 -f /proj/snic2021-2-4/private/herring/users/sabine/software/3d-dna-master/lift/lift-input-mnd-to-asm-mnd.awk <(awk '$0~/^>/{$1=substr($1,2); print}' juicebox/pin_HiC_run3.assembly) <(awk '$0!~/^>/' juicebox/pin_HiC_run3.assembly) juicebox/Charengus_HiCPacBio_sorted_dedup_filter.sorted.links.mnd > temp.pin_HiC_run3.asm_mnd.txt'I hope you can please help out.
thanks a lot,
myo