Could not read hic file: null ,error with run-asm-pipeline.sh

[Zoey1001]

Dear developers, when i run the "run-asm-pipline.sh" ,encountered these errors and i hope you can give me some suggestions. nohup.out: temp.scaffolds.0.asm_mnd.txt does not exist or does not contain any reads. Could not read hic file: null :( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting! Could not read hic file: null :( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting! mv: cannot stat 'depletion_score_wide.wig': No such file or directory mv: cannot stat 'depletion_score_narrow.wig': No such file or directory mv: cannot stat 'mismatch_wide.bed': No such file or directory mv: cannot stat 'mismatch_narrow.bed': No such file or directory mv: cannot stat 'coverage_wide.wig': No such file or directory mv: cannot stat 'repeats_wide.bed': No such file or directory cat: mismatch_narrow.at.step.0.bed: No such file or directory cat: repeats_wide.at.step.0.bed: No such file or directory temp.scaffolds.1.asm_mnd.txt does not exist or does not contain any reads. Could not read hic file: null :( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting! Could not read hic file: null :( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting! mv: cannot stat 'depletion_score_wide.wig': No such file or directory mv: cannot stat 'depletion_score_narrow.wig': No such file or directory mv: cannot stat 'mismatch_wide.bed': No such file or directory mv: cannot stat 'mismatch_narrow.bed': No such file or directory mv: cannot stat 'coverage_wide.wig': No such file or directory mv: cannot stat 'repeats_wide.bed': No such file or directory cat: mismatch_narrow.at.step.1.bed: No such file or directory cat: repeats_wide.at.step.1.bed: No such file or directory temp.scaffolds.2.asm_mnd.txt does not exist or does not contain any reads. :( No resolved files are found. Please rerun the pipeline to include the scaffold segment. Exiting!

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run-asm-pipeline.log /home/dell/1k_spider/biotools/3d-dna-master/run-asm-pipeline.sh -r 2 scaffolds.fasta merged_nodups.txt version: 180922 -r|--rounds flag was triggered, will run 2 round(s) of misjoin correction. ############### 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: scaffolds.0.cprops ...Using merged_nodups file: scaffolds.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 ...detecting misjoins in round 0 assembly: :) -p flag was triggered. Running with GNU Parallel support parameter set to true. :) -c flag was triggered, starting calculations with 5% saturation level :) -w flag was triggered, performing cursory search for mismatches at 12500 resolution :) -d flag was triggered, depletion score will be averaged across a region bounded by 62500 superdiagonal :) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold :) -n flag was triggered, performing mismatch region thinning at 500 resolution ...Dumping 12500 resolution matrix :) -w flag was triggered, performing cursory search for repeat at 12500 resolution :) -t flag was triggered, flagging regions with coverage higher than 2 ...Dumping 12500 resolution coverage track ...-p flag was triggered. Running with GNU Parallel support parameter set to true. ...-r flag was triggered, output will be labeled as .1. ...applying edits to cprops file ...applying edits to mnd file ...starting round 1 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: scaffolds.1.cprops ...Using merged_nodups file: scaffolds.mnd.1.txt ...Scaffolding all scaffolds and contigs greater or equal to 15000 bp. ...Starting iteration # 1 :) DONE! ...visualizing round 1 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 ...detecting misjoins in round 1 assembly: :) -p flag was triggered. Running with GNU Parallel support parameter set to true. :) -c flag was triggered, starting calculations with 5% saturation level :) -w flag was triggered, performing cursory search for mismatches at 12500 resolution :) -d flag was triggered, depletion score will be averaged across a region bounded by 62500 superdiagonal :) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold :) -n flag was triggered, performing mismatch region thinning at 500 resolution ...Dumping 12500 resolution matrix :) -w flag was triggered, performing cursory search for repeat at 12500 resolution :) -t flag was triggered, flagging regions with coverage higher than 2 ...Dumping 12500 resolution coverage track ...-p flag was triggered. Running with GNU Parallel support parameter set to true. ...-r flag was triggered, output will be labeled as .2. ...applying edits to cprops file ...applying edits to mnd file ...starting round 2 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: scaffolds.2.cprops ...Using merged_nodups file: scaffolds.mnd.2.txt ...Scaffolding all scaffolds and contigs greater or equal to 15000 bp. ...Starting iteration # 1 :) DONE! ...visualizing round 2 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

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(base) dell@dell-PowerEdge-R940xa:~/1k_spider/biotools/zq/aligned$ ls abnormal.sam collisions.txt header inter.hic inter.txt merged_sort.txt unmapped.sam collisions_nodups.txt dups.txt inter_30.txt inter_hists.m merged_nodups.txt opt_dups.txt (base) dell@dell-PowerEdge-R940xa:~/1k_spider/biotools/zq/aligned$

[Zoey1001]

These are the files generated by juicer.sh (base) dell@dell-PowerEdge-R940xa:/1k_spider/biotools/zq/aligned$ ls abnormal.sam collisions.txt header inter.hic inter.txt merged_sort.txt unmapped.sam collisions_nodups.txt dups.txt inter_30.txt inter_hists.m merged_nodups.txt opt_dups.txt (base) dell@dell-PowerEdge-R940xa:/1k_spider/biotools/zq/aligned$

[dudcha]

Hi, Make sure that your merged_nodups was generated with the right fasta reference and that you have permissions to read the files. Based on the messages either 1) the headers in the fasta and mnd are different or mnd/fasta is empty/unreadable. Best, -Olga

[netwon123]

could u solve this bug?****

[primatehao]

Dear developers, I also met this problem and then I checked my merged_nodups and header. I ensure that the files are correct. There is still this error when I run the "run-asm-pipline.sh". I hope you respond. Thanks!