./run-asm-pipeline.sh -m diploid merged_nodups.txt polish.fasta

[hzaumsq]

...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 500000 resolution :) -d flag was triggered, depletion score will be averaged across a region bounded by 1000000 superdiagonal :) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold :) -n flag was triggered, performing mismatch region thinning at 1000 resolution ...Dumping 500000 resolution matrix 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! :) -w flag was triggered, performing cursory search for repeat at 500000 resolution :) -t flag was triggered, flagging regions with coverage higher than 2 ...Dumping 500000 resolution coverage track 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 awk: fatal: cannot open file merged_nodups.txt.0_asm.superscaf_track.txt' for reading (No such file or directory) awk: /public/msq/3DDNA/3d-dna-master/edit/overlay-edits.awk:20: fatal: cannot open file merged_nodups.txt.0_asm.scaffold_track.txt' for reading (No such file or directory) :) No more input edits to be done. Moving to polishing! :( No resolved files are found. Please rerun the pipeline to include the scaffold segment. Exiting!

[dudcha]

Hello hzaumsq,

I am not sure what is your question here, but it seems that the Hi-C map was not created: Could not read hic file: null. Check your dev/stdout for Java message regarding this.

Best, Olga

[Huangtianyu-caas]

Hi hzaumsq ,

Did you solve this issue? I have got the same problem.

Best, Tianyu

[hzaumsq]

chmod 777 run-asm-pipeline.sh

[Huangtianyu-caas]

chmod 777 run-asm-pipeline.sh

Hi hzaumsq,

Thanks for your prompt reply.

I have tried this, the attributes of run-asm-pipeline.sh is -rwxrwxrwx. But still reported the same error.

Best, Tianyu

[licheng0921]

Hi Tianyu,

I also meet the same error.

Have you fixed this error?

Best, licheng