**************************
*****BioNano Genomics*****
******BNG-NGS Merge*******
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ExportAGP.pl 11203 2020-06-18 21:28:10Z jwang

Running on host: 783e65a4b2e8

Process ID (PID): 997
Start time: 2023-01-20 15:22:06

COMMAND
perl /home/bionano/tools/access/1.0/../../pipeline/1.0/HybridScaffold/1.0/hybridScaffold.pl -c hybridScaffold_DLE1_config_082522.xml -b EXP_REFINEFINAL1.cmap -n Borneo.hap1.hic.filtered.fasta -u CTTAAG -z cur_results_10235353.zip -w status_10235353.txt -B 2 -N 2 -f -g -r /home/bionano/tools/access/1.0/../../pipeline/1.0/RefAligner/1.0/RefAligner -p /home/bionano/tools/access/1.0/../../pipeline/1.0/Pipeline/1.0 -o /home/bionano/access/local/jobs/10235353/output

NGS file: /home/bionano/access/local/jobs/10235353/Borneo.hap1.hic.filtered.fasta 
BNG file: /home/bionano/access/local/jobs/10235353/EXP_REFINEFINAL1.cmap 
Configuration file: /home/bionano/access/local/jobs/10235353/hybridScaffold_DLE1_config_082522.xml 
Output folder: /home/bionano/access/local/jobs/10235353/output
RefAligner binary: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner

Beginning FASTA to CMAP conversion...
Using Enzyme: CTTAAG
Minimum Length: 0 Kb
Minimum Labels: 0
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/fa2cmap_multi_color.pl -i /home/bionano/access/local/jobs/10235353/Borneo.hap1.hic.filtered.fasta -m 0 -M 0 -o /home/bionano/access/local/jobs/10235353/output/fa2cmap -e CTTAAG 1
key file /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_key.txt
FASTA to CMAP conversion complete in 14 seconds.

Beginning FASTA header conversion...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/fa_key_convert.pl /home/bionano/access/local/jobs/10235353/Borneo.hap1.hic.filtered.fasta /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in 9 seconds.

New FASTA with CMAP Ids as headers: /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap

Beginning initial NGS CMAP to BioNano CMAP alignment...
Running command: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -ref /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10235353/EXP_REFINEFINAL1.cmap -o align0 -stdout -stderr -maxmem 128 -maxthreads 64 -maxvirtmem 0 -maxmemIncrease 8 -RAmem 3 1 0.9 -M 1 3 -ScaleDelta 0.03 2 -ScaleDeltaBPP -hashScaleDelta 2 -res 2.6 -resSD 0.8 -FP 0.2 -FN 0.02 -sf 0.10 -sd 0.0 -sr 0.01 -se 0.2 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 11 2.4 1.4 0.05 3.0 1 1 1 -hash -hashdelta 27 -hashoffset 1 -hashrange 0 -hashGrouped 6 11 900 -hashMultiMatch 50 2 -hashGC 300 -hashT2 1 -hashkeys 1 -HSDrange 1.0 -insertThreads 4 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -resEstimate -f -mres 0.9 -thetaScale 0.5 -KL 1.5 -KF 1.5 -Kmax 4 -MinFN 0.01 -MinFP 0.16 -MinSF 0.05 -MaxSF 0.15 -MinSD 0.0 -MaxSD 0.0 -MinSR 0.007 -MaxSR 0.015 -MaxSE 0.5 -MinRes 2.0 -MinResSD 0.8 -hashSD 0 1 -hashSR 0 1
Initial alignment complete in 20 seconds.

Rescaling BioNano CMAP...
Running command: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -merge -i /home/bionano/access/local/jobs/10235353/EXP_REFINEFINAL1.cmap -o /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust -readparameters /home/bionano/access/local/jobs/10235353/output/align0/align0.errbin -stdout -stderr
Rescaling complete in 1 second.

Beginning initial NGS CMAP to rescaled BioNano CMAP alignment...
Running command: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -ref /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap -o align1 -stdout -stderr -maxmem 128 -maxthreads 64 -maxvirtmem 0 -maxmemIncrease 8 -RAmem 3 1 0.9 -ScaleDelta 0.03 1 -ScaleDeltaBPP -hashScaleDelta 2 -res 2.6 -resSD 0.8 -FP 0.2 -FN 0.02 -sf 0.10 -sd 0.0 -sr 0.01 -se 0.2 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.4 0.05 3.0 1 1 3 -hash -hashdelta 46 -hashoffset 1 -hashrange 0 -hashGC 300 -hashT2 1 -hashkeys 1 -hashGrouped 5 7 900 -hashMultiMatch 50 15 -insertThreads 4 -HSDrange 1.0 -nosplit 2 -biaswt 0 -T 1e-10 -S 0.1 -A 11 -L 60 -F 0.20 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 120 -resEstimate -MultiMatches 10 -MultiMatchesFilter 2 -RefSplitStitch 1 -RefSplit 0 120 1 -MultiMatchesUniqueQuery 5 0 2 1 -MultiMatchesUniqueRef 5 0 2 1 -RepeatMask 2 0.01 -RepeatRec 0.6 0.6 1.4 2 0.9 -f -mres 0.9 -thetaScale 0.5 -KL 1.5 -KF 1.5 -Kmax 4 -hashSD 0 1 -hashSR 0 1
Initial rescaled alignment complete in 54 seconds.

32 alignments found between /home/bionano/access/local/jobs/10235353/Borneo.hap1.hic.filtered.fasta and /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap

Beginning AssignAlignType...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/AssignAlignType.pl /home/bionano/access/local/jobs/10235353/output/align1/align1.xmap /home/bionano/access/local/jobs/10235353/output/align1/align1_r.cmap /home/bionano/access/local/jobs/10235353/output/align1/align1_q.cmap /home/bionano/access/local/jobs/10235353/output/assignAlignType/assignAlignType.xmap /home/bionano/access/local/jobs/10235353/output/assignAlignType/assignAlignType_r.cmap /home/bionano/access/local/jobs/10235353/output/assignAlignType/assignAlignType_q.cmap 11 5 /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap /home/bionano/access/local/jobs/10235353/output/assignAlignType/conflicts.txt 30
AssignAlignType complete in 5 seconds.
0 BNG contigs have been flagged as conflicting
0 NGS contigs have been flagged as conflicting

Beginning cut_conflicts...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/cut_conflicts.pl -align1XmapFile /home/bionano/access/local/jobs/10235353/output/align1/align1.xmap -align1GMFile /home/bionano/access/local/jobs/10235353/output/align1/align1_q.cmap -align1SeqFile /home/bionano/access/local/jobs/10235353/output/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap -oriSeqFile /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap -conflictFile /home/bionano/access/local/jobs/10235353/output/assignAlignType/conflicts.txt -outDir /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts -outGMFile /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -outSeqFile /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -windowSize 10000 -qScoreThreshold 35 -covThreshold 10 -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner
cut_conflicts complete in 5 seconds.
30 BNG contigs are found after the cut-conflict step
97 NGS contigs are found after the cut-conflict step

Beginning MergeNGS_BN...
*Using conflict-cut BioNano and conflict-cut sequence CMAP*
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/MergeNGS_BN.pl -outputDir /home/bionano/access/local/jobs/10235353/output/mergeNGS_BN -refaligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -logFile mergeNGS_BN_script.log -ngs_cmap_fn /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -bng_cmap_fn /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -id_shift 100000 -readparameters /home/bionano/access/local/jobs/10235353/output/align1/align1.errbin -xmlFile /home/bionano/access/local/jobs/10235353/hybridScaffold_DLE1_config_082522.xml
MergeNGS_BN complete in 21 seconds.

Beginning extraction of used and not used NGS contigs in hybrid scaffold pairmerge step...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/find_used_not_used_ngs.pl /home/bionano/access/local/jobs/10235353/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_cut.cmap /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner
Extraction of NGS contigs complete in 1 second.

Beginning alignment of NGS cmap to Hybrid CMAP...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/align_final_seq_two_passes.pl -outDir /home/bionano/access/local/jobs/10235353/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10235353/hybridScaffold_DLE1_config_082522.xml -seqFile /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10235353/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10235353/output/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 55 seconds.

Beginning extraction of used and not used BNG contigs in hybrid scaffold pairmerge step...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/find_used_not_used_bn.pl /home/bionano/access/local/jobs/10235353/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner
Extraction of BNG contigs complete in 1 second.

Beginning alignment of BNG cmap to Hybrid CMAP...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/align_final_bng.pl -outDir /home/bionano/access/local/jobs/10235353/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10235353/hybridScaffold_DLE1_config_082522.xml -bngFile /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10235353/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10235353/output/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 56 seconds.

Merging Hybrid CMAP with NGS not participated in the hybrid scaffold...
Running command: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -f -i /home/bionano/access/local/jobs/10235353/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10235353/output/mergeNGS_BN/all_not_used_ngs.cmap -o HYBRID_SCAFFOLD_notUsedNGS_merged -merge -minsites 0 -stdout -stderr
Merging Hybrid CMAP with naive NGS CMAP complete in no time.

Merging Hybrid CMAP with BNG CMAP not participated in the hybrid scaffold...
Running command: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -f -i /home/bionano/access/local/jobs/10235353/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10235353/output/mergeNGS_BN/all_not_used_bng.cmap -o HYBRID_SCAFFOLD_notUsedBNG_merged -merge -stdout -stderr
Merging Hybrid CMAP with naive BNG CMAP complete in 1 second.

Beginnning construction of AGP and FASTA file of the scaffolded and unscaffolded sequences...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/ExportAGP.pl -i /home/bionano/access/local/jobs/10235353/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /home/bionano/access/local/jobs/10235353/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /home/bionano/access/local/jobs/10235353/output/agp_fasta -m /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_key.txt -s /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered.fasta -e CTTAAG 1 -r /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/auto_cut_NGS_coord_translation.txt -t
AGP and FASTA generation complete in 41 seconds.

Calculating statistics...

Original BioNano Genome Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/EXP_REFINEFINAL1.cmap

Count  = 30
Min length (Mbp) = 1.264
Median length (Mbp) = 9.322
Mean length (Mbp) = 16.102
N50 length (Mbp) = 34.917
Max length (Mbp) = 42.949
Total length (Mbp) = 483.065

Bpp-adjusted BioNano Genome Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap

Count  = 30
Min length (Mbp) = 1.264
Median length (Mbp) = 9.323
Mean length (Mbp) = 16.104
N50 length (Mbp) = 34.920
Max length (Mbp) = 42.952
Total length (Mbp) = 483.106

Original NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/fa2cmap/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels.cmap

Count  = 97
Min length (Mbp) = 0.071
Median length (Mbp) = 0.176
Mean length (Mbp) = 4.949
N50 length (Mbp) = 29.940
Max length (Mbp) = 45.874
Total length (Mbp) = 480.031

Conflict Resolution from BNG-NGS alignment:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_conflicts_cut_stats.pl /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/conflicts_cut_status.txt

Number of conflict cuts made to Bionano maps: 0
Number of conflict cuts made to NGS sequences: 0
Number of Bionano maps to be cut: 0
Number of NGS sequences to be cut: 0

Before merge: BioNano Genome Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap

Count  = 30
Min length (Mbp) = 1.264
Median length (Mbp) = 9.323
Mean length (Mbp) = 16.104
N50 length (Mbp) = 34.920
Max length (Mbp) = 42.952
Total length (Mbp) = 483.106

Before merge: NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/assignAlignType/cut_conflicts/Borneo.hap1.hic.filtered_CTTAAG_0kb_0labels_cut.cmap

Count  = 97
Min length (Mbp) = 0.071
Median length (Mbp) = 0.176
Mean length (Mbp) = 4.949
N50 length (Mbp) = 29.940
Max length (Mbp) = 45.874
Total length (Mbp) = 480.031

BNG Genome Map in hybrid scaffold statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 27
Min length (Mbp) = 1.264
Median length (Mbp) = 9.920
Mean length (Mbp) = 17.643
N50 length (Mbp) = 34.920
Max length (Mbp) = 42.952
Total length (Mbp) = 476.367

NGS sequences in hybrid scaffold (CMAP) statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 26
Min length (Mbp) = 0.140
Median length (Mbp) = 16.256
Mean length (Mbp) = 17.944
N50 length (Mbp) = 30.875
Max length (Mbp) = 45.874
Total length (Mbp) = 466.540

Hybrid scaffold Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align_final/step2.hybrid.cmap

Count  = 16
Min length (Mbp) = 0.267
Median length (Mbp) = 36.463
Mean length (Mbp) = 29.787
N50 length (Mbp) = 41.396
Max length (Mbp) = 48.260
Total length (Mbp) = 476.585

NGS FASTA sequence in hybrid scaffold statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_scaffolded_seq_fasta_stats.pl /home/bionano/access/local/jobs/10235353/output/agp_fasta/Borneo.hap1.hic.filtered.fasta.cut.fasta /home/bionano/access/local/jobs/10235353/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 26
Min length (Mbp) = 0.049
Median length (Mbp) = 16.256
Mean length (Mbp) = 17.924
N50 length (Mbp) = 30.875
Max length (Mbp) = 45.874
Total length (Mbp) = 466.030

Hybrid scaffold FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_fasta_stats.pl /home/bionano/access/local/jobs/10235353/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 16
Min length (Mbp) = 0.140
Median length (Mbp) = 34.992
Mean length (Mbp) = 29.131
N50 length (Mbp) = 41.271
Max length (Mbp) = 48.170
Total length (Mbp) = 466.095

Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_hybrid_scaffold_not_scaffolded_seq_fasta_stats.pl /home/bionano/access/local/jobs/10235353/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /home/bionano/access/local/jobs/10235353/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 91
Min length (Mbp) = 0.011
Median length (Mbp) = 0.160
Mean length (Mbp) = 5.276
N50 length (Mbp) = 41.271
Max length (Mbp) = 48.170
Total length (Mbp) = 480.096


Calculating CMAP statistics complete in 17 seconds.

Calculating XMAP statistics...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
8	21411749.2	20944076.3	20944076.3	97.82
5	34941272.9	34895999.1	34895999.1	99.87
100002	41395874.6	41295802.3	41295802.3	99.76
100003	39240816.1	34934521.6	34934521.6	89.03
1	45909026.2	45811595.9	45811595.9	99.79
14	34365747.4	34168314.9	34160031.6	99.40
2	43270216.4	43087955.9	43087955.9	99.58
7	46663922.7	46397692	46397692	99.43
100024	4349162.6	102313.5	102313.5	2.35
9	48259774.8	48102213.8	48102213.8	99.67
100015	9561496.8	9539504.7	9539504.7	99.77
100001	42952451.6	42838107.7	42836783.8	99.73
10	19960999.3	19902836.9	19902836.9	99.71
4	37985399.6	37816717	37816717	99.56
100020	6050613.3	4888815.8	4888815.8	80.80
41	266624.0	378781	263131	98.69

Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10235353/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap1_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
8	21411749.2	21367497.2	21301898.2	99.49
4	37985399.6	37816717	37816717	99.56
41	266624.0	0	0	0.00
9	48259774.8	47886069.9	47830705.9	99.11
2	43270216.4	43229238.5	43191379.5	99.82
14	34365747.4	34314194.6	34314194.6	99.85
7	46663922.7	46658048.5	46584441	99.83
1	45909026.2	45886141.4	45886141.4	99.95
10	19960999.3	19870516.9	19870516.9	99.55
100020	6050613.3	6033569.8	6033569.8	99.72
100015	9561496.8	9539504.7	9539504.7	99.77
100001	42952451.6	42836783.8	42836783.8	99.73
100003	39240816.1	39227254.7	39227254.7	99.97
5	34941272.9	34900555.6	34900555.6	99.88
100002	41395874.6	41389189.9	41389189.9	99.98
100024	4349162.6	4332962.1	4332962.1	99.63

XMAP statistics calculation complete in 1 second.

Beginning archive and zip of result files...
