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

Running on host: 2561ab1ccf1d

Process ID (PID): 997
Start time: 2023-01-26 17:52:08

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 Calcutta4.hap2.hic.filtered.fasta -u CTTAAG -z cur_results_10236014.zip -w status_10236014.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/10236014/output

NGS file: /home/bionano/access/local/jobs/10236014/Calcutta4.hap2.hic.filtered.fasta 
BNG file: /home/bionano/access/local/jobs/10236014/EXP_REFINEFINAL1.cmap 
Configuration file: /home/bionano/access/local/jobs/10236014/hybridScaffold_DLE1_config_082522.xml 
Output folder: /home/bionano/access/local/jobs/10236014/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/10236014/Calcutta4.hap2.hic.filtered.fasta -m 0 -M 0 -o /home/bionano/access/local/jobs/10236014/output/fa2cmap -e CTTAAG 1
key file /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_key.txt
FASTA to CMAP conversion complete in 13 seconds.

Beginning FASTA header conversion...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/fa_key_convert.pl /home/bionano/access/local/jobs/10236014/Calcutta4.hap2.hic.filtered.fasta /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in 4 seconds.

New FASTA with CMAP Ids as headers: /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.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/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10236014/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 23 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/10236014/EXP_REFINEFINAL1.cmap -o /home/bionano/access/local/jobs/10236014/output/align0/EXP_REFINEFINAL1_bppAdjust -readparameters /home/bionano/access/local/jobs/10236014/output/align0/align0.errbin -stdout -stderr
Rescaling complete in no time.

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/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10236014/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 42 seconds.

47 alignments found between /home/bionano/access/local/jobs/10236014/Calcutta4.hap2.hic.filtered.fasta and /home/bionano/access/local/jobs/10236014/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/10236014/output/align1/align1.xmap /home/bionano/access/local/jobs/10236014/output/align1/align1_r.cmap /home/bionano/access/local/jobs/10236014/output/align1/align1_q.cmap /home/bionano/access/local/jobs/10236014/output/assignAlignType/assignAlignType.xmap /home/bionano/access/local/jobs/10236014/output/assignAlignType/assignAlignType_r.cmap /home/bionano/access/local/jobs/10236014/output/assignAlignType/assignAlignType_q.cmap 11 5 /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap /home/bionano/access/local/jobs/10236014/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap /home/bionano/access/local/jobs/10236014/output/assignAlignType/conflicts.txt 30
AssignAlignType complete in 5 seconds.
1 BNG contigs have been flagged as conflicting
1 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/10236014/output/align1/align1.xmap -align1GMFile /home/bionano/access/local/jobs/10236014/output/align1/align1_q.cmap -align1SeqFile /home/bionano/access/local/jobs/10236014/output/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /home/bionano/access/local/jobs/10236014/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap -oriSeqFile /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap -conflictFile /home/bionano/access/local/jobs/10236014/output/assignAlignType/conflicts.txt -outDir /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts -outGMFile /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -outSeqFile /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/Calcutta4.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 5 seconds.
41 BNG contigs are found after the cut-conflict step
105 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/10236014/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/10236014/output/assignAlignType/cut_conflicts/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -bng_cmap_fn /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -id_shift 100000 -readparameters /home/bionano/access/local/jobs/10236014/output/align1/align1.errbin -xmlFile /home/bionano/access/local/jobs/10236014/hybridScaffold_DLE1_config_082522.xml
MergeNGS_BN complete in 25 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/10236014/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/Calcutta4.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/10236014/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_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/10236014/hybridScaffold_DLE1_config_082522.xml -seqFile /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10236014/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10236014/output/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 42 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/10236014/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10236014/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/10236014/output/align_final -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_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/10236014/hybridScaffold_DLE1_config_082522.xml -bngFile /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10236014/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10236014/output/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 41 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/10236014/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10236014/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 1 second.

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/10236014/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10236014/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 no time.

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/10236014/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /home/bionano/access/local/jobs/10236014/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /home/bionano/access/local/jobs/10236014/output/agp_fasta -m /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_key.txt -s /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered.fasta -e CTTAAG 1 -r /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/auto_cut_NGS_coord_translation.txt -t
AGP and FASTA generation complete in 10 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/10236014/EXP_REFINEFINAL1.cmap

Count  = 41
Min length (Mbp) = 0.514
Median length (Mbp) = 8.110
Mean length (Mbp) = 11.593
N50 length (Mbp) = 19.188
Max length (Mbp) = 48.837
Total length (Mbp) = 475.329

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/10236014/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap

Count  = 41
Min length (Mbp) = 0.515
Median length (Mbp) = 8.114
Mean length (Mbp) = 11.598
N50 length (Mbp) = 19.196
Max length (Mbp) = 48.858
Total length (Mbp) = 475.528

Original NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236014/output/fa2cmap/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels.cmap

Count  = 104
Min length (Mbp) = 0.071
Median length (Mbp) = 0.325
Mean length (Mbp) = 4.692
N50 length (Mbp) = 15.036
Max length (Mbp) = 43.145
Total length (Mbp) = 487.955

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/10236014/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: 1
Number of Bionano maps to be cut: 0
Number of NGS sequences to be cut: 1

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/10236014/output/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap

Count  = 41
Min length (Mbp) = 0.515
Median length (Mbp) = 8.114
Mean length (Mbp) = 11.598
N50 length (Mbp) = 19.196
Max length (Mbp) = 48.858
Total length (Mbp) = 475.528

Before merge: NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236014/output/assignAlignType/cut_conflicts/Calcutta4.hap2.hic.filtered_CTTAAG_0kb_0labels_cut.cmap

Count  = 105
Min length (Mbp) = 0.071
Median length (Mbp) = 0.327
Mean length (Mbp) = 4.647
N50 length (Mbp) = 15.036
Max length (Mbp) = 43.145
Total length (Mbp) = 487.955

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/10236014/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 39
Min length (Mbp) = 0.515
Median length (Mbp) = 9.465
Mean length (Mbp) = 12.135
N50 length (Mbp) = 19.196
Max length (Mbp) = 48.858
Total length (Mbp) = 473.263

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/10236014/output/align_final/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 49
Min length (Mbp) = 0.136
Median length (Mbp) = 8.627
Mean length (Mbp) = 9.688
N50 length (Mbp) = 15.036
Max length (Mbp) = 43.145
Total length (Mbp) = 474.730

Hybrid scaffold Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236014/output/align_final/step2.hybrid.cmap

Count  = 22
Min length (Mbp) = 0.288
Median length (Mbp) = 19.074
Mean length (Mbp) = 21.671
N50 length (Mbp) = 33.856
Max length (Mbp) = 48.858
Total length (Mbp) = 476.764

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/10236014/output/agp_fasta/Calcutta4.hap2.hic.filtered.fasta.cut.fasta /home/bionano/access/local/jobs/10236014/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 48
Min length (Mbp) = 0.288
Median length (Mbp) = 8.652
Mean length (Mbp) = 9.886
N50 length (Mbp) = 15.036
Max length (Mbp) = 43.145
Total length (Mbp) = 474.546

Hybrid scaffold FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_fasta_stats.pl /home/bionano/access/local/jobs/10236014/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 22
Min length (Mbp) = 0.288
Median length (Mbp) = 19.016
Mean length (Mbp) = 21.578
N50 length (Mbp) = 33.797
Max length (Mbp) = 48.690
Total length (Mbp) = 474.716

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/10236014/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /home/bionano/access/local/jobs/10236014/output/agp_fasta/EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 85
Min length (Mbp) = 0.000
Median length (Mbp) = 0.202
Mean length (Mbp) = 5.743
N50 length (Mbp) = 33.797
Max length (Mbp) = 48.690
Total length (Mbp) = 488.124


Calculating CMAP statistics complete in 13 seconds.

Calculating XMAP statistics...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10236014/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
100002	44363574.4	44293506.2	44275381	99.80
1	43163878.9	43081395.5	43081395.5	99.81
100022	7987247.2	7942259.1	7942259.1	99.44
14	19650272.2	19215094.8	19215094.8	97.79
20	17085216.6	16997531.6	16997531.6	99.49
21	10693177.7	10646371.3	10646371.3	99.56
7	34072686.3	33944702.5	33944702.5	99.62
16	44236505.4	44138549.1	44138549.1	99.78
100001	48857703.2	48562511.8	48559340.3	99.39
15	29097994.7	28522278.6	28522278.6	98.02
100019	9695547.4	9630066.2	9630066.2	99.32
11	33855740.5	33761632.7	33761632.7	99.72
56	287669.0	389418	278449	96.79
19	11334852.0	11316937	11316937	99.84
4	23106839.8	23041877	23041877	99.72
12	29229100.0	29125881.9	29125881.9	99.65
100004	32005505.2	31894336.3	31894336.3	99.65
100014	12709368.5	12256709.4	12256709.4	96.44
100009	18497255.7	18433505.7	18433505.7	99.66
100034	1470512.7	1147598.2	1147598.2	78.04
31	3495120.0	3284310.6	3284310.6	93.97
100030	1868545.8	1787636	1787636	95.67

Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10236014/output/align_final EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_Calcutta4_hap2_hic_filtered_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
7	34072686.3	34974717.4	34023239.4	99.85
100009	18497255.7	18489798.1	18489798.1	99.96
11	33855740.5	31092990.1	31085758.6	91.82
100002	44363574.4	44275381	44275381	99.80
15	29097994.7	29020171.8	28929869.2	99.42
21	10693177.7	10675243.7	10675243.7	99.83
1	43163878.9	43018774.5	42996403.5	99.61
20	17085216.6	17070007.6	17070007.6	99.91
16	44236505.4	42503428.1	42503428.1	96.08
19	11334852.0	11316937	11316937	99.84
100014	12709368.5	12698456.6	12698456.6	99.91
12	29229100.0	29209356.8	29186503.8	99.85
100030	1868545.8	1823596.3	1823596.3	97.59
31	3495120.0	3471640.6	3416725.1	97.76
100034	1470512.7	1386725.8	1386725.8	94.30
100001	48857703.2	48736248.4	48736248.4	99.75
56	287669.0	0	0	0.00
100022	7987247.2	7978240.2	7978240.2	99.89
4	23106839.8	23049395.6	23049395.6	99.75
100004	32005505.2	31948514.9	31948514.9	99.82
100019	9695547.4	9651896.7	9651896.7	99.55
14	19650272.2	19235502.4	19235502.4	97.89

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
