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

Running on host: 606644df5a7c

Process ID (PID): 997
Start time: 2023-01-20 15:22:55

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.hap2.hic.filtered.fasta -u CTTAAG -z cur_results_10235354.zip -w status_10235354.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/10235354/output

NGS file: /home/bionano/access/local/jobs/10235354/Borneo.hap2.hic.filtered.fasta 
BNG file: /home/bionano/access/local/jobs/10235354/EXP_REFINEFINAL1.cmap 
Configuration file: /home/bionano/access/local/jobs/10235354/hybridScaffold_DLE1_config_082522.xml 
Output folder: /home/bionano/access/local/jobs/10235354/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/10235354/Borneo.hap2.hic.filtered.fasta -m 0 -M 0 -o /home/bionano/access/local/jobs/10235354/output/fa2cmap -e CTTAAG 1
key file /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.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/10235354/Borneo.hap2.hic.filtered.fasta /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in 7 seconds.

New FASTA with CMAP Ids as headers: /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.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/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10235354/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 21 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/10235354/EXP_REFINEFINAL1.cmap -o /home/bionano/access/local/jobs/10235354/output/align0/EXP_REFINEFINAL1_bppAdjust -readparameters /home/bionano/access/local/jobs/10235354/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/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10235354/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 57 seconds.

37 alignments found between /home/bionano/access/local/jobs/10235354/Borneo.hap2.hic.filtered.fasta and /home/bionano/access/local/jobs/10235354/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/10235354/output/align1/align1.xmap /home/bionano/access/local/jobs/10235354/output/align1/align1_r.cmap /home/bionano/access/local/jobs/10235354/output/align1/align1_q.cmap /home/bionano/access/local/jobs/10235354/output/assignAlignType/assignAlignType.xmap /home/bionano/access/local/jobs/10235354/output/assignAlignType/assignAlignType_r.cmap /home/bionano/access/local/jobs/10235354/output/assignAlignType/assignAlignType_q.cmap 11 5 /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap /home/bionano/access/local/jobs/10235354/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap /home/bionano/access/local/jobs/10235354/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/10235354/output/align1/align1.xmap -align1GMFile /home/bionano/access/local/jobs/10235354/output/align1/align1_q.cmap -align1SeqFile /home/bionano/access/local/jobs/10235354/output/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /home/bionano/access/local/jobs/10235354/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap -oriSeqFile /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -conflictFile /home/bionano/access/local/jobs/10235354/output/assignAlignType/conflicts.txt -outDir /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts -outGMFile /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -outSeqFile /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/Borneo.hap2.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 4 seconds.
34 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/10235354/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/10235354/output/assignAlignType/cut_conflicts/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -bng_cmap_fn /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -id_shift 100000 -readparameters /home/bionano/access/local/jobs/10235354/output/align1/align1.errbin -xmlFile /home/bionano/access/local/jobs/10235354/hybridScaffold_DLE1_config_082522.xml
MergeNGS_BN complete in 23 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/10235354/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/Borneo.hap2.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/10235354/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_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/10235354/hybridScaffold_DLE1_config_082522.xml -seqFile /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10235354/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10235354/output/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 1 minute and 1 second.

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/10235354/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10235354/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/10235354/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_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/10235354/hybridScaffold_DLE1_config_082522.xml -bngFile /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10235354/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10235354/output/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 39 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/10235354/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10235354/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/10235354/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10235354/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/10235354/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /home/bionano/access/local/jobs/10235354/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /home/bionano/access/local/jobs/10235354/output/agp_fasta -m /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_key.txt -s /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered.fasta -e CTTAAG 1 -r /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/auto_cut_NGS_coord_translation.txt -t
AGP and FASTA generation complete in 55 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/10235354/EXP_REFINEFINAL1.cmap

Count  = 34
Min length (Mbp) = 0.158
Median length (Mbp) = 9.164
Mean length (Mbp) = 13.695
N50 length (Mbp) = 21.662
Max length (Mbp) = 51.101
Total length (Mbp) = 465.646

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/10235354/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap

Count  = 34
Min length (Mbp) = 0.158
Median length (Mbp) = 9.164
Mean length (Mbp) = 13.696
N50 length (Mbp) = 21.662
Max length (Mbp) = 51.102
Total length (Mbp) = 465.653

Original NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235354/output/fa2cmap/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap

Count  = 97
Min length (Mbp) = 0.071
Median length (Mbp) = 0.214
Mean length (Mbp) = 5.006
N50 length (Mbp) = 28.134
Max length (Mbp) = 51.135
Total length (Mbp) = 485.570

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/10235354/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/10235354/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap

Count  = 34
Min length (Mbp) = 0.158
Median length (Mbp) = 9.164
Mean length (Mbp) = 13.696
N50 length (Mbp) = 21.662
Max length (Mbp) = 51.102
Total length (Mbp) = 465.653

Before merge: NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235354/output/assignAlignType/cut_conflicts/Borneo.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap

Count  = 97
Min length (Mbp) = 0.071
Median length (Mbp) = 0.214
Mean length (Mbp) = 5.006
N50 length (Mbp) = 28.134
Max length (Mbp) = 51.135
Total length (Mbp) = 485.570

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/10235354/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 34
Min length (Mbp) = 0.158
Median length (Mbp) = 9.164
Mean length (Mbp) = 13.696
N50 length (Mbp) = 21.662
Max length (Mbp) = 51.102
Total length (Mbp) = 465.653

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/10235354/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 31
Min length (Mbp) = 0.093
Median length (Mbp) = 10.161
Mean length (Mbp) = 15.266
N50 length (Mbp) = 28.134
Max length (Mbp) = 51.135
Total length (Mbp) = 473.248

Hybrid scaffold Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10235354/output/align_final/step2.hybrid.cmap

Count  = 15
Min length (Mbp) = 0.955
Median length (Mbp) = 41.393
Mean length (Mbp) = 31.800
N50 length (Mbp) = 43.771
Max length (Mbp) = 51.203
Total length (Mbp) = 477.004

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/10235354/output/agp_fasta/Borneo.hap2.hic.filtered.fasta.cut.fasta /home/bionano/access/local/jobs/10235354/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 28
Min length (Mbp) = 0.286
Median length (Mbp) = 13.192
Mean length (Mbp) = 16.890
N50 length (Mbp) = 28.134
Max length (Mbp) = 51.135
Total length (Mbp) = 472.915

Hybrid scaffold FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_fasta_stats.pl /home/bionano/access/local/jobs/10235354/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 15
Min length (Mbp) = 0.521
Median length (Mbp) = 41.332
Mean length (Mbp) = 31.563
N50 length (Mbp) = 43.645
Max length (Mbp) = 51.135
Total length (Mbp) = 473.441

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/10235354/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /home/bionano/access/local/jobs/10235354/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 87
Min length (Mbp) = 0.005
Median length (Mbp) = 0.153
Mean length (Mbp) = 5.587
N50 length (Mbp) = 43.645
Max length (Mbp) = 51.135
Total length (Mbp) = 486.096


Calculating CMAP statistics complete in 16 seconds.

Calculating XMAP statistics...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10235354/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
9	41393444.9	40760273.8	40760273.8	98.47
7	25660427.1	25566700.4	25566700.4	99.63
26	955103.0	1127673	953680	99.85
10	43938596.8	43878030	43878030	99.86
6	46718046.1	46497570.3	46497570.3	99.53
15	12878698.0	12838405	12838405	99.69
8	21676612.7	21628619.3	21628619.3	99.78
3	45793676.2	45691372.6	45691372.6	99.78
100003	43770889.6	43636368.1	43636368.1	99.69
1	51203484.8	51076636.6	51076636.6	99.75
2	48755665.0	48698202	48698202	99.88
5	43379273.0	43248553.8	43206917.8	99.60
100014	12777564.9	12728465.5	12723346.2	99.58
100028	3492889.7	726709.4	726709.4	20.81
11	34609901.9	34452509.7	34452509.7	99.55

Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10235354/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Borneo_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
100028	3492889.7	3472741.1	3472741.1	99.42
6	46718046.1	46646174.2	46646174.2	99.85
7	25660427.1	25514374.4	25514374.4	99.43
1	51203484.8	51201572	51154561	99.90
8	21676612.7	21673815.9	21673815.9	99.99
11	34609901.9	31598084.4	31598084.4	91.30
10	43938596.8	37844159.8	37770033.8	85.96
9	41393444.9	41306470.4	41306470.4	99.79
100003	43770889.6	43686852.8	43686852.8	99.81
2	48755665.0	48006654	48006654	98.46
15	12878698.0	12313834	12299582	95.50
3	45793676.2	45676404.6	45676404.6	99.74
5	43379273.0	43268783.6	43268783.6	99.75
100014	12777564.9	12723346.2	12723346.2	99.58
26	955103.0	0	0	0.00

XMAP statistics calculation complete in 1 second.

Beginning archive and zip of result files...
