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

Running on host: 61433275c4eb

Process ID (PID): 997
Start time: 2023-01-11 02:01:57

COMMAND
perl /home/bionano/tools/access/1.0/../../pipeline/1.0/HybridScaffold/1.0/hybridScaffold.pl -c hybridScaffold_DLE1_config_082522.xml -b Paliama.golden.cmap -n Paliama.contigs2.fasta -u CTTAAG -z cur_results_10234698.zip -w status_10234698.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/10234698/output

NGS file: /home/bionano/access/local/jobs/10234698/Paliama.contigs2.fasta 
BNG file: /home/bionano/access/local/jobs/10234698/Paliama.golden.cmap 
Configuration file: /home/bionano/access/local/jobs/10234698/hybridScaffold_DLE1_config_082522.xml 
Output folder: /home/bionano/access/local/jobs/10234698/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/10234698/Paliama.contigs2.fasta -m 0 -M 0 -o /home/bionano/access/local/jobs/10234698/output/fa2cmap -e CTTAAG 1
key file /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels_key.txt
FASTA to CMAP conversion complete in 18 seconds.

Beginning FASTA header conversion...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/fa_key_convert.pl /home/bionano/access/local/jobs/10234698/Paliama.contigs2.fasta /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels_key.txt
FASTA header conversion complete in 9 seconds.

New FASTA with CMAP Ids as headers: /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels_CmapIdHeaders.fa
NGS map path: /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_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/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10234698/Paliama.golden.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 12 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/10234698/Paliama.golden.cmap -o /home/bionano/access/local/jobs/10234698/output/align0/Paliama_golden_bppAdjust -readparameters /home/bionano/access/local/jobs/10234698/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/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels.cmap -i /home/bionano/access/local/jobs/10234698/output/align0/Paliama_golden_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 47 seconds.

20 alignments found between /home/bionano/access/local/jobs/10234698/Paliama.contigs2.fasta and /home/bionano/access/local/jobs/10234698/output/align0/Paliama_golden_bppAdjust.cmap

Beginning AssignAlignType...
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/AssignAlignType.pl /home/bionano/access/local/jobs/10234698/output/align1/align1.xmap /home/bionano/access/local/jobs/10234698/output/align1/align1_r.cmap /home/bionano/access/local/jobs/10234698/output/align1/align1_q.cmap /home/bionano/access/local/jobs/10234698/output/assignAlignType/assignAlignType.xmap /home/bionano/access/local/jobs/10234698/output/assignAlignType/assignAlignType_r.cmap /home/bionano/access/local/jobs/10234698/output/assignAlignType/assignAlignType_q.cmap 11 5 /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels.cmap /home/bionano/access/local/jobs/10234698/output/align0/Paliama_golden_bppAdjust.cmap /home/bionano/access/local/jobs/10234698/output/assignAlignType/conflicts.txt 30
AssignAlignType complete in 6 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/10234698/output/align1/align1.xmap -align1GMFile /home/bionano/access/local/jobs/10234698/output/align1/align1_q.cmap -align1SeqFile /home/bionano/access/local/jobs/10234698/output/align1/align1_r.cmap -maxOverhang 10 -breakPointFileShiftAmount 30 -oriGMFile /home/bionano/access/local/jobs/10234698/output/align0/Paliama_golden_bppAdjust.cmap -oriSeqFile /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels.cmap -conflictFile /home/bionano/access/local/jobs/10234698/output/assignAlignType/conflicts.txt -outDir /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts -outGMFile /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama_golden_bppAdjust_cut.cmap -outSeqFile /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama.contigs2_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 6 seconds.
16 BNG contigs are found after the cut-conflict step
80 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/10234698/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/10234698/output/assignAlignType/cut_conflicts/Paliama.contigs2_CTTAAG_0kb_0labels_cut.cmap -bng_cmap_fn /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama_golden_bppAdjust_cut.cmap -id_shift 100000 -readparameters /home/bionano/access/local/jobs/10234698/output/align1/align1.errbin -xmlFile /home/bionano/access/local/jobs/10234698/hybridScaffold_DLE1_config_082522.xml
MergeNGS_BN complete in 22 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/10234698/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama.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/10234698/output/align_final -outFilePrefix Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10234698/hybridScaffold_DLE1_config_082522.xml -seqFile /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama.contigs2_CTTAAG_0kb_0labels_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10234698/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10234698/output/align_final/align_final_seq_script_log.txt
align sequences to hybrid scaffolds completed  in 1 minute and 4 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/10234698/output/mergeNGS_BN 100000 /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama_golden_bppAdjust_cut.cmap /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner
Extraction of BNG contigs complete in 2 seconds.

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/10234698/output/align_final -outFilePrefix Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD -refAligner /home/bionano/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12642rel/RefAligner -xmlFile /home/bionano/access/local/jobs/10234698/hybridScaffold_DLE1_config_082522.xml -bngFile /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama_golden_bppAdjust_cut.cmap -scaffoldFile /home/bionano/access/local/jobs/10234698/output/align_final/step2.hybrid.cmap -logFile /home/bionano/access/local/jobs/10234698/output/align_final/align_final_bng_log.txt
align Bionano genome maps to hybrid scaffolds completed  in 1 minute.

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/10234698/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10234698/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/10234698/output/align_final/step2.hybrid.cmap -i /home/bionano/access/local/jobs/10234698/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/10234698/output/align_final/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap -c /home/bionano/access/local/jobs/10234698/output/align_final/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_r.cmap -o /home/bionano/access/local/jobs/10234698/output/agp_fasta -m /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels_key.txt -s /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2.fasta -e CTTAAG 1 -r /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/auto_cut_NGS_coord_translation.txt -t
AGP and FASTA generation complete in 44 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/10234698/Paliama.golden.cmap

Count  = 16
Min length (Mbp) = 1.498
Median length (Mbp) = 44.322
Mean length (Mbp) = 38.581
N50 length (Mbp) = 55.996
Max length (Mbp) = 62.397
Total length (Mbp) = 617.288

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/10234698/output/align0/Paliama_golden_bppAdjust.cmap

Count  = 16
Min length (Mbp) = 1.234
Median length (Mbp) = 36.514
Mean length (Mbp) = 31.784
N50 length (Mbp) = 46.131
Max length (Mbp) = 51.405
Total length (Mbp) = 508.539

Original NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10234698/output/fa2cmap/Paliama.contigs2_CTTAAG_0kb_0labels.cmap

Count  = 80
Min length (Mbp) = 0.072
Median length (Mbp) = 0.387
Mean length (Mbp) = 6.149
N50 length (Mbp) = 33.488
Max length (Mbp) = 50.699
Total length (Mbp) = 491.945

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/10234698/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/10234698/output/assignAlignType/cut_conflicts/Paliama_golden_bppAdjust_cut.cmap

Count  = 16
Min length (Mbp) = 1.234
Median length (Mbp) = 36.514
Mean length (Mbp) = 31.784
N50 length (Mbp) = 46.131
Max length (Mbp) = 51.405
Total length (Mbp) = 508.539

Before merge: NGS sequences statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10234698/output/assignAlignType/cut_conflicts/Paliama.contigs2_CTTAAG_0kb_0labels_cut.cmap

Count  = 80
Min length (Mbp) = 0.072
Median length (Mbp) = 0.387
Mean length (Mbp) = 6.149
N50 length (Mbp) = 33.488
Max length (Mbp) = 50.699
Total length (Mbp) = 491.945

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/10234698/output/align_final/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 14
Min length (Mbp) = 7.801
Median length (Mbp) = 39.842
Mean length (Mbp) = 36.021
N50 length (Mbp) = 46.131
Max length (Mbp) = 51.405
Total length (Mbp) = 504.298

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/10234698/output/align_final/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_q.cmap

Count  = 37
Min length (Mbp) = 0.072
Median length (Mbp) = 8.202
Mean length (Mbp) = 12.956
N50 length (Mbp) = 33.488
Max length (Mbp) = 50.699
Total length (Mbp) = 479.380

Hybrid scaffold Map statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl ./scripts/calc_cmap_stats.pl /home/bionano/access/local/jobs/10234698/output/align_final/step2.hybrid.cmap

Count  = 12
Min length (Mbp) = 0.316
Median length (Mbp) = 46.963
Mean length (Mbp) = 41.867
N50 length (Mbp) = 47.794
Max length (Mbp) = 51.764
Total length (Mbp) = 502.400

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/10234698/output/agp_fasta/Paliama.contigs2.fasta.cut.fasta /home/bionano/access/local/jobs/10234698/output/agp_fasta/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 36
Min length (Mbp) = 0.072
Median length (Mbp) = 8.288
Mean length (Mbp) = 13.304
N50 length (Mbp) = 33.488
Max length (Mbp) = 50.699
Total length (Mbp) = 478.940

Hybrid scaffold FASTA statistics:
Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_fasta_stats.pl /home/bionano/access/local/jobs/10234698/output/agp_fasta/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta

Count  = 12
Min length (Mbp) = 0.316
Median length (Mbp) = 44.879
Mean length (Mbp) = 40.159
N50 length (Mbp) = 46.463
Max length (Mbp) = 50.699
Total length (Mbp) = 481.907

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/10234698/output/agp_fasta/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta /home/bionano/access/local/jobs/10234698/output/agp_fasta/Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

Count  = 64
Min length (Mbp) = 0.016
Median length (Mbp) = 0.218
Mean length (Mbp) = 7.733
N50 length (Mbp) = 45.604
Max length (Mbp) = 50.699
Total length (Mbp) = 494.912


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/10234698/output/align_final Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
100003	49312661.5	49034601.9	49034601.9	99.44
100008	37694799.8	36990931.8	36936914.5	97.99
100001	51404705.2	51318692.3	51287385.9	99.77
6	42179477.4	42012592.4	41995139.8	99.56
100004	48676605.7	48588702.2	48588702.2	99.82
100002	49806101.1	49639609.1	49639609.1	99.67
100006	46130765.4	44024360.6	44024360.6	95.43
100007	41988615.8	41913048.3	41903617.5	99.80
43	315965.0	369040.5	299402.5	94.76
1	51763630.9	51668295.7	51668295.7	99.82
100005	47794246.7	47693184.7	47693184.7	99.79
100009	35332910.7	35322349.3	35270807.7	99.82

Running command: /home/bionano2/.conda/envs/bionano3/bin/perl scripts/calc_xmap_stats.pl /home/bionano/access/local/jobs/10234698/output/align_final Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap step2.hybrid.cmap Paliama_golden_bppAdjust_cmap_Paliama_contigs2_fasta_BNGcontigs_HYBRID_SCAFFOLD.xmap.stats

refContig	refContig_size	query_cov_bp	query_unique_cov_bp	query_unique_cov_percent
100002	49806101.1	49726569	49726569	99.84
100001	51404705.2	51317356.6	51317356.6	99.83
100003	49312661.5	49245397.2	49245397.2	99.86
100008	37694799.8	37587507.1	37587507.1	99.72
6	42179477.4	42402027.4	42122726.4	99.87
100004	48676605.7	48588702.2	48588702.2	99.82
43	315965.0	0	0	0.00
1	51763630.9	51019325.7	51019325.7	98.56
100006	46130765.4	46067096.9	46067096.9	99.86
100009	35332910.7	35270807.7	35270807.7	99.82
100005	47794246.7	47706738.1	47706738.1	99.82
100007	41988615.8	41915849.1	41915849.1	99.83

XMAP statistics calculation complete in no time.

Beginning archive and zip of result files...
