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

Running on host: 8d814f93f346

Process ID (PID): 997
Start time: 2023-01-30 14:58:52

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 SH3217.hap1.contigs2.fasta -u CTTAAG -z cur_results_10236089_10236342.zip -w status_10236089_10236342.txt -M conflicts_cut_status_CTTAAG_10236089_10236342.txt -g -B 2 -N 2 -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/10236342/output

NGS file: /home/bionano/access/local/jobs/10236342/output/fa2cmap/SH3217.hap1.contigs2.fasta 
BNG file: /home/bionano/access/local/jobs/10236342/EXP_REFINEFINAL1.cmap 
Configuration file: /home/bionano/access/local/jobs/10236342/hybridScaffold_DLE1_config_082522.xml 
Output folder: /home/bionano/access/local/jobs/10236342/output
User-defined conflict status file: /home/bionano/access/local/jobs/10236342/conflicts_cut_status_CTTAAG_10236089_10236342.txt
RefAligner binary: /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner

Beginning cut_conflicts based on input a conflict file...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/cut_conflicts.pl -oriGMFile /home/bionano/access/local/jobs/10236342/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap -oriSeqFile /home/bionano/access/local/jobs/10236342/output/fa2cmap/SH3217.hap1.contigs2_CTTAAG_0kb_0labels.cmap -outDir /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1 -outGMFile /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/EXP_REFINEFINAL1_bppAdjust_cut.cmap -outSeqFile /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/SH3217.hap1.contigs2_CTTAAG_0kb_0labels_cut.cmap -modBkptStatusFile /home/bionano/access/local/jobs/10236342/conflicts_cut_status_CTTAAG_10236089_10236342.txt -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner
cut_conflicts complete in 3 seconds.
25 BNG contigs are found after the cut-conflict step
103 NGS contigs are found after the cut-conflict step

Beginning MergeNGS_BN...
*Using user-defined conflict-cut BioNano and sequence CMAP files*
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/MergeNGS_BN.pl -outputDir /home/bionano/access/local/jobs/10236342/output/mergeNGS_BN_M1 -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/10236342/output/assignAlignType/cut_conflicts_M1/SH3217.hap1.contigs2_CTTAAG_0kb_0labels_cut.cmap -bng_cmap_fn /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/EXP_REFINEFINAL1_bppAdjust_cut.cmap -id_shift 100000 -readparameters /home/bionano/access/local/jobs/10236342/output/align1/align1.errbin -xmlFile /home/bionano/access/local/jobs/10236342/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/10236342/output/mergeNGS_BN_M1 100000 /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/SH3217.hap1.contigs2_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/10236342/output/align_final_M1 -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10236342/hybridScaffold_DLE1_config_082522.xml -seqFile /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/SH3217.hap1.contigs2_CTTAAG_0kb_0labels_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10236342/output/align_final_M1/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10236342/output/align_final_M1/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 1 minute and 7 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/10236342/output/mergeNGS_BN_M1 100000 /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/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/10236342/output/align_final_M1 -outFilePrefix EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10236342/hybridScaffold_DLE1_config_082522.xml -bngFile /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/EXP_REFINEFINAL1_bppAdjust_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10236342/output/align_final_M1/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10236342/output/align_final_M1/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 35 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/10236342/output/align_final_M1/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10236342/output/mergeNGS_BN_M1/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/10236342/output/align_final_M1/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10236342/output/mergeNGS_BN_M1/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/10236342/output/align_final_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /home/bionano/access/local/jobs/10236342/output/align_final_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /home/bionano/access/local/jobs/10236342/output/agp_fasta_M1 -m /home/bionano/access/local/jobs/10236342/output/fa2cmap/SH3217.hap1.contigs2_CTTAAG_0kb_0labels_key.txt -s /home/bionano/access/local/jobs/10236342/output/fa2cmap/SH3217.hap1.contigs2.fasta -e CTTAAG 1 -r /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/auto_cut_NGS_coord_translation.txt -t
AGP and FASTA generation complete in 46 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/10236342/EXP_REFINEFINAL1.cmap

Count  = 30
Min length (Mbp) = 0.354
Median length (Mbp) = 11.206
Mean length (Mbp) = 16.484
N50 length (Mbp) = 35.541
Max length (Mbp) = 49.949
Total length (Mbp) = 494.527

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/10236342/output/align0/EXP_REFINEFINAL1_bppAdjust.cmap

Count  = 30
Min length (Mbp) = 0.354
Median length (Mbp) = 11.201
Mean length (Mbp) = 16.477
N50 length (Mbp) = 35.526
Max length (Mbp) = 49.928
Total length (Mbp) = 494.322

Original NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236342/output/fa2cmap/SH3217.hap1.contigs2_CTTAAG_0kb_0labels.cmap

Count  = 111
Min length (Mbp) = 0.071
Median length (Mbp) = 0.234
Mean length (Mbp) = 4.560
N50 length (Mbp) = 26.285
Max length (Mbp) = 46.682
Total length (Mbp) = 506.170

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/10236342/output/assignAlignType/cut_conflicts_M1/conflicts_cut_status.txt

Number of conflict cuts made to Bionano maps: 0
Number of conflict cuts made to NGS sequences: 4
Number of Bionano maps to be cut: 0
Number of NGS sequences to be cut: 4

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/10236342/output/assignAlignType/cut_conflicts_M1/EXP_REFINEFINAL1_bppAdjust_cut.cmap

Count  = 25
Min length (Mbp) = 0.354
Median length (Mbp) = 16.813
Mean length (Mbp) = 19.621
N50 length (Mbp) = 35.526
Max length (Mbp) = 49.928
Total length (Mbp) = 490.534

Before merge: NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236342/output/assignAlignType/cut_conflicts_M1/SH3217.hap1.contigs2_CTTAAG_0kb_0labels_cut.cmap

Count  = 103
Min length (Mbp) = 0.041
Median length (Mbp) = 0.204
Mean length (Mbp) = 4.877
N50 length (Mbp) = 26.285
Max length (Mbp) = 46.682
Total length (Mbp) = 502.372

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/10236342/output/align_final_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 22
Min length (Mbp) = 0.354
Median length (Mbp) = 21.066
Mean length (Mbp) = 22.188
N50 length (Mbp) = 35.526
Max length (Mbp) = 49.928
Total length (Mbp) = 488.128

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/10236342/output/align_final_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 37
Min length (Mbp) = 0.132
Median length (Mbp) = 7.835
Mean length (Mbp) = 13.195
N50 length (Mbp) = 26.285
Max length (Mbp) = 46.682
Total length (Mbp) = 488.227

Hybrid scaffold Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10236342/output/align_final_M1/step2.hybrid.cmap

Count  = 13
Min length (Mbp) = 0.588
Median length (Mbp) = 46.491
Mean length (Mbp) = 37.597
N50 length (Mbp) = 47.788
Max length (Mbp) = 58.819
Total length (Mbp) = 488.760

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/10236342/output/agp_fasta_M1/SH3217.hap1.contigs2.fasta.cut.fasta /home/bionano/access/local/jobs/10236342/output/agp_fasta_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 32
Min length (Mbp) = 0.185
Median length (Mbp) = 11.635
Mean length (Mbp) = 15.221
N50 length (Mbp) = 26.285
Max length (Mbp) = 46.682
Total length (Mbp) = 487.059

Hybrid scaffold FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_fasta_stats.pl /home/bionano/access/local/jobs/10236342/output/agp_fasta_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 13
Min length (Mbp) = 0.588
Median length (Mbp) = 46.455
Mean length (Mbp) = 37.534
N50 length (Mbp) = 47.805
Max length (Mbp) = 58.790
Total length (Mbp) = 487.946

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/10236342/output/agp_fasta_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /home/bionano/access/local/jobs/10236342/output/agp_fasta_M1/EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 98
Min length (Mbp) = 0.000
Median length (Mbp) = 0.168
Mean length (Mbp) = 5.174
N50 length (Mbp) = 47.805
Max length (Mbp) = 58.790
Total length (Mbp) = 507.056


Calculating CMAP statistics complete in 18 seconds.

Calculating XMAP statistics...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10236342/output/align_final_M1 EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
7	35741225.3	35361125	35361125	98.94
2	51406602.5	51334808.8	51334808.8	99.86
34	588414.0	942324.5	584991	99.42
10	35675149.7	35710014.9	35606898.9	99.81
3	47788044.2	47640609.5	47640609.5	99.69
8	47055996.2	46974957.2	46974957.2	99.83
22	48273695.0	47881896.8	47881896.8	99.19
19	8376619.5	8495457.2	8154063.6	97.34
100007	35083094.8	34996889.9	34996889.9	99.75
4	58818645.5	58280952.8	58154693.8	98.87
9	23532950.8	23487069.5	23487069.5	99.81
100001	49928447.0	49838489	49838489	99.82
11	46491087.3	46362106.9	46362106.9	99.72

Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10236342/output/align_final_M1 EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap EXP_REFINEFINAL1_bppAdjust_cmap_SH3217_hap1_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
19	8376619.5	8103978.2	7930804	94.68
34	588414.0	0	0	0.00
8	47055996.2	47002526.1	47002526.1	99.89
3	47788044.2	47381986.9	47331998.9	99.05
9	23532950.8	23487069.5	23487069.5	99.81
100001	49928447.0	49846437.2	49846437.2	99.84
100007	35083094.8	35005148.9	35005148.9	99.78
2	51406602.5	51169811.7	51169811.7	99.54
10	35675149.7	35640004.7	35640004.7	99.90
22	48273695.0	48232192	48232192	99.91
7	35741225.3	35692276.8	35692276.8	99.86
4	58818645.5	59031663	58742173.5	99.87
11	46491087.3	46385733	46385733	99.77

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
