/mnt/storage/home/vsfishman/Distr/3d-dna/run-asm-pipeline.sh -r 1 /mnt/storage/home/vsfishman/Distr/juicer-master/juicer-wd/references/sciara_merged_Prim_on_Gerbi_soft_WG.fasta /mnt/storage/home/vsfishman/tmp/sciara/aligned/merged_nodups.txt
version: 180922
 -r|--rounds flag was triggered, will run 1 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 false.
:) -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: sciara_merged_Prim_on_Gerbi_soft_WG.0.cprops
...Using merged_nodups file: sciara_merged_Prim_on_Gerbi_soft_WG.mnd.0.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
...Starting iteration # 2
...Starting iteration # 3
...Starting iteration # 4
...Starting iteration # 5
...Starting iteration # 6
...Starting iteration # 7
...Starting iteration # 8
...Starting iteration # 9
...Starting iteration # 10
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...Starting iteration # 14
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...Starting iteration # 16
...Starting iteration # 17
...Starting iteration # 18
...Starting iteration # 19
...Starting iteration # 20
...Starting iteration # 21
...Starting iteration # 22
...Starting iteration # 23
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...Starting iteration # 25
...Starting iteration # 26
...Starting iteration # 27
...Starting iteration # 28
...Starting iteration # 29
...Starting iteration # 30
...Starting iteration # 31
...Starting iteration # 32
...Starting iteration # 33
...Starting iteration # 34
...Starting iteration # 35
...Starting iteration # 36
...Starting iteration # 37
...Starting iteration # 38
...Starting iteration # 39
:) DONE!
...visualizing round 0 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -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
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Calculating norms for zoom BP_1000
Writing expected
Writing norms
Finished writing norms
...detecting misjoins in round 0 assembly:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 25000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 125000 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 25000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Coarse resolution saturation level = 3.5341
...Analyzing near-diagonal mismatches
...Filtering mismatch calls without better alternative: Not functional yet, skipping
...Thinning mismatch region boundaries.
...Dumping 1000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Fine resolution saturation level = 1
...Analyzing near-diagonal mismatches
:) -w flag was triggered, performing cursory search for repeat at 25000 resolution
:) -t flag was triggered, flagging regions with coverage higher than 2
...Dumping 25000 resolution coverage track
HiC file version: 8
...-p flag was triggered. Running with GNU Parallel support parameter set to false.
...-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 false.
:) -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: sciara_merged_Prim_on_Gerbi_soft_WG.1.cprops
...Using merged_nodups file: sciara_merged_Prim_on_Gerbi_soft_WG.mnd.1.txt
...Scaffolding all scaffolds and contigs greater or equal to 15000 bp.
...Starting iteration # 1
...Starting iteration # 2
...Starting iteration # 3
...Starting iteration # 4
...Starting iteration # 5
...Starting iteration # 6
...Starting iteration # 7
...Starting iteration # 8
...Starting iteration # 9
...Starting iteration # 10
...Starting iteration # 11
...Starting iteration # 12
...Starting iteration # 13
...Starting iteration # 14
...Starting iteration # 15
...Starting iteration # 16
...Starting iteration # 17
...Starting iteration # 18
...Starting iteration # 19
...Starting iteration # 20
...Starting iteration # 21
...Starting iteration # 22
...Starting iteration # 23
...Starting iteration # 24
...Starting iteration # 25
...Starting iteration # 26
...Starting iteration # 27
...Starting iteration # 28
...Starting iteration # 29
...Starting iteration # 30
...Starting iteration # 31
...Starting iteration # 32
...Starting iteration # 33
...Starting iteration # 34
...Starting iteration # 35
...Starting iteration # 36
...Starting iteration # 37
...Starting iteration # 38
...Starting iteration # 39
...Starting iteration # 40
...Starting iteration # 41
...Starting iteration # 42
...Starting iteration # 43
...Starting iteration # 44
:) DONE!
...visualizing round 1 results:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -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
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Calculating norms for zoom BP_1000
Writing expected
Writing norms
Finished writing norms
###############
Starting polish:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -q flag was triggered, performing polishing taking into account signal with minimum 1 mapping quality
...-j flag was triggered, will use Juicebox map sciara_merged_Prim_on_Gerbi_soft_WG.resolved.hic
...-a flag was triggered, will use scaffold annotation file sciara_merged_Prim_on_Gerbi_soft_WG.resolved_asm.scaffold_track.txt
...-b flag was triggered, will use superscaffold annotation file sciara_merged_Prim_on_Gerbi_soft_WG.resolved_asm.superscaf_track.txt
...-s flag was triggered, will ignore all scaffolds shorter than 1000000 for polishing
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 100000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 3000000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 100000 resolution
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -d flag was triggered, depletion score will be averaged across a region bounded by 3000000 superdiagonal
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 100000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Coarse resolution saturation level = 4.52849
...Analyzing near-diagonal mismatches
...Filtering mismatch calls without better alternative: Not functional yet, skipping
...Thinning mismatch region boundaries.
...Dumping 1000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Fine resolution saturation level = 1
...Analyzing near-diagonal mismatches
...-p flag was triggered. Running with GNU Parallel support parameter set to false.
...-r flag was triggered, output will be labeled as *.polish.*
...applying edits to cprops file
...applying edits to mnd file
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to false.
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
:) -s flag was triggered, starting calculations with 1000000 threshold starting contig/scaffold size
...Using cprops file: sciara_merged_Prim_on_Gerbi_soft_WG.resolved.polish.cprops
...Using merged_nodups file: sciara_merged_Prim_on_Gerbi_soft_WG.resolved.polish.mnd.txt
...Explicit scaffold set has been listed as input. Using set as a first iteration.
...Starting iteration # 1
...Starting iteration # 2
...Starting iteration # 3
...Starting iteration # 4
...Starting iteration # 5
:) DONE!
:) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to false.
:) -q flag was triggered, starting calculations with 1 threshold mapping quality
:) -s flag was triggered, starting calculations with 1000000 threshold starting contig/scaffold size
...Using cprops file: sciara_merged_Prim_on_Gerbi_soft_WG.resolved.polish.cprops
...Using merged_nodups file: sciara_merged_Prim_on_Gerbi_soft_WG.resolved.polish.mnd.txt
...Explicit scaffold set has been listed as input. Using set as a first iteration.
...Starting iteration # 1
...Starting iteration # 2
:) DONE!
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -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
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Calculating norms for zoom BP_1000
Writing expected
Writing norms
Finished writing norms
###############
Starting split:
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
...-q flag was triggered, will ignore all reads with mapping quality less then 1 for polishing
...-j flag was triggered, will use Juicebox map sciara_merged_Prim_on_Gerbi_soft_WG.polished.hic
...-a flag was triggered, will use scaffold annotation file sciara_merged_Prim_on_Gerbi_soft_WG.polished_asm.scaffold_track.txt
...-b flag was triggered, will use superscaffold annotation file sciara_merged_Prim_on_Gerbi_soft_WG.polished_asm.superscaf_track.txt
...-s flag was triggered, will ignore all scaffolds shorter than 100000 for polishing
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 100000 resolution
:) -d flag was triggered, depletion score will be averaged across a region bounded by 3000000 superdiagonal
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -c flag was triggered, starting calculations with 5% saturation level
:) -w flag was triggered, performing cursory search for mismatches at 100000 resolution
:) -k flag was triggered, starting calculations with 55% depletion as mismatch threshold
:) -d flag was triggered, depletion score will be averaged across a region bounded by 3000000 superdiagonal
:) -n flag was triggered, performing mismatch region thinning at 1000 resolution
...Dumping 100000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Coarse resolution saturation level = 4.53887
...Analyzing near-diagonal mismatches
...Filtering mismatch calls without better alternative: Not functional yet, skipping
...Thinning mismatch region boundaries.
...Dumping 1000 resolution matrix
HiC file version: 8
...Estimating necessary saturation level for requested misassembly sensitivity
...Fine resolution saturation level = 1
...Analyzing near-diagonal mismatches
...-p flag was triggered. Running with GNU Parallel support parameter set to false.
...-r flag was triggered, output will be labeled as *.split.*
...applying edits to cprops file
...applying edits to mnd file
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -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
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Calculating norms for zoom BP_1000
Writing expected
Writing norms
Finished writing norms
###############
Starting sealing:
... -i flag was triggered, will attempt to place back only debris contigs/scaffolds and those less than 15000
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
:) -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
Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess
HiC file version: 8

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Calculating norms for zoom BP_1000
Writing expected
Writing norms
Finished writing norms
###############
Finilizing output:
... -s flag was triggered, treating all contigs/scaffolds shorter than 15000 as unattempted.
... -l flag was triggered. Output will appear with headers of the form sciara_merged_Prim_on_Gerbi_soft_WG_hic_scaffold_#.
... -g flag was triggered, making gap size between scaffolded draft sequences to be equal to 500.
Analyzing the merged assembly
...trimming N overhangs
...adding gaps