Last login: Tue May 13 15:56:41 on ttys000 Kimberlys-MacBook-Pro:~ kimberlydavis$ cd Desktop/VICUNA_v1.3/ Kimberlys-MacBook-Pro:VICUNA_v1.3 kimberlydavis$ OMP_NUM_THREADS=8 ./ bin/vicuna-omp-v1.0 config/test_configure.txt -------------------------------------------------------Program runs with the following Parameter setting: ===== Trimmer ===== vectorFileName trimLogFileName minMSize 9 minInternalMSize 15 maxOverhangSize 2 minReadSize 25 ===== Profiler ===== MSAFileName binNumber kmerLength maxHD 1 minSpan 75 blockNumber rMapFileName

20 15 (encode using 4 bytes) 5

===== Contiger ===== w1 12 w2 5 Divergence 8 max_read_overhang min_profile_col_weight min_consensus_base_ratio max_contig_overhang seed_kmer_len 12 min_contig_overlap min_contig_links 3 min_identity 90 min_perc_polymorphism max_variant_len 20

2 5 85 10 25 5

===== Assembly ===== pFqDir /Users/kimberlydavis/Desktop/Test_vicuna batchSize 1000000 LibSizeLowerBound 100 LibSizeUpperBound 800 min_output_contig_len 200

outputDIR vicuna_output/

/Users/kimberlydavis/Desktop/Test_vicuna/

-------------------------------------------------------Indexing ... /Users/kimberlydavis/Desktop/Test_vicuna/PR8_paired_1.fq /Users/kimberlydavis/Desktop/Test_vicuna/PR8_paired_2.fq PR8_paired_1.fq #reads: 544305 PR8_paired_2.fq #reads: 544305 Total # Input Reads: 1088610 Indexing done !!!

*** 0.0231581 mins ***

----------------------------------------------------------Trimming ... no vector trimming applied. Writing trim logs to file: /Users/kimberlydavis/Desktop/ Test_vicuna/vicuna_output/trim.log Number of Reads Trimmed by Heads, Tails, Full, Total: 0(nan%total) 0(nan%total) 0(nan%total) 0 Number of low complexity reads: 54 Number of trimmed read-pairs: 0 ( nan %total) Trimming done !!!

*** 0.070797 mins ***

----------------------------------------------------------No MSA file specified, Profiler Skipped Profiling done !!!

*** 6.99361e-07 mins ***

----------------------------------------------------------Building Contigs ... create super shingles for 1088610 reads *** 0.390479 mins *** Clustering via super-shingles *** 0.0247653 mins ***

Init contigs no. initial contigs: 112499 no. reads involved: 943205 *** 0.153325 mins *** seed_template = 1101101111100110000111111 STable size: 134290 no. contigs: 112902 no. reads involved: 1088149 *** 0.334335 mins *** Validate contigs Segmentation fault: 11 Kimberlys-MacBook-Pro:VICUNA_v1.3 kimberlydavis$

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Last login: Tue May 13 15:56:41 on ttys000. Kimberlys-MacBook-Pro:~ kimberlydavis$ cd Desktop/VICUNA_v1.3/. Kimberlys-MacBook-Pro:VICUNA_v1.3 ...
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