2025-Jan-22 12:51:35.658901 Assembly begins. Command line: shasta --threads 64 --input ../inputs/fragment_cov.reads.fasta --config Nanopore-r10.4.1_e8.2-400bps_sup-Herro-Sep2024 --Kmers.k 20 --Kmers.probability 0.1 --Align.minAlignedFraction 0.8 --ReadGraph.strandSeparationMethod 0 --MinHash.minFrequency 10 --Align.minAlignedMarkerCount 500 For options in use for this assembly, see shasta.conf in the assembly directory. This run uses options "--memoryBacking 4K --memoryMode anonymous". This could result in longer run time. For faster assembly, use "--memoryBacking 2M --memoryMode filesystem" (root privilege via sudo required). Therefore the results of this run should not be used for the purpose of benchmarking assembly time. However the memory options don't affect assembly results in any way. This assembly will use 64 threads. Discarded read statistics for file /scratch.ssd/sivico26/job_8384136.pbs-m1.metacentrum.cz/inputs/fragment_cov.reads.fasta: Discarded 0 reads containing invalid bases for a total 0 valid bases. Discarded 6478152 reads shorter than 10000 bases for a total 38466817514 bases. Discarded 0 reads containing repeat counts 256 or more for a total 0 bases. Discarded read statistics for all input files: Discarded 0 reads containing invalid bases for a total 0 valid bases. Discarded 6478152 short reads for a total 38466817514 bases. Discarded 0 reads containing repeat counts 256 or more for a total 0 bases. Read statistics for reads that will be used in this assembly: Total number of reads is 12588286. Total number of raw bases is 217506847281. Average read length is 17278.5 bases. N50 for read length is 20000 bases. Found 0 reads with duplicate names. Discarded from the assembly 0 reads with duplicate names. Flagged 17940 reads as palindromic out of 12588286 total. Palindromic fraction is 0.00142513 log2MinHashBucketCount reduced from 34 to maximum allowed value 31. LowHash0 algorithm will use 2^31 = 2147483648 buckets. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 0: high frequency 173182247, total 801289120, capacity 801289120. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 1: high frequency 346911912, total 1015124061, capacity 1480673184. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 2: high frequency 436485453, total 1184571149, capacity 1702102231. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 3: high frequency 491175293, total 1331941044, capacity 1874870295. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 4: high frequency 528106534, total 1456694301, capacity 2030434184. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 5: high frequency 556298977, total 1584382086, capacity 2193765868. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 6: high frequency 578113019, total 1697402929, capacity 2345687741. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 7: high frequency 596064710, total 1808660646, capacity 2498320116. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 8: high frequency 611167838, total 1914223589, capacity 2645742224. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 9: high frequency 624163854, total 2014483108, capacity 2786983371. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 10: high frequency 635214178, total 2101523056, capacity 2911681205. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 11: high frequency 645494141, total 2192734890, capacity 3041345909. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 12: high frequency 654734681, total 2279315786, capacity 3165128847. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 13: high frequency 663034843, total 2362676563, capacity 3284782140. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 14: high frequency 670699943, total 2442237750, capacity 3399380068. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 15: high frequency 677861909, total 2518598843, capacity 3509459144. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 16: high frequency 684488086, total 2591962260, capacity 3615008785. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 17: high frequency 690705076, total 2662088447, capacity 3715846215. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 18: high frequency 696344742, total 2723593193, capacity 3804889687. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 19: high frequency 701754945, total 2785582503, capacity 3894683484. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 20: high frequency 707097844, total 2848311390, capacity 3985457099. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 21: high frequency 712011803, total 2905853450, capacity 4068798059. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 22: high frequency 716787843, total 2961137620, capacity 4148412291. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 23: high frequency 721391757, total 3014559255, capacity 4225915616. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 24: high frequency 725861451, total 3068620160, capacity 4304136895. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 25: high frequency 729971522, total 3115817155, capacity 4372460771. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 26: high frequency 734289444, total 3166604721, capacity 4445711671. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 27: high frequency 738337482, total 3212659147, capacity 4512209079. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 28: high frequency 742414216, total 3260356525, capacity 4581455352. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 29: high frequency 746412876, total 3306549569, capacity 4648716015. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 30: high frequency 750324475, total 3350652447, capacity 4712837313. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 31: high frequency 754205917, total 3393650462, capacity 4774831572. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 32: high frequency 757893243, total 3432234301, capacity 4831131432. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 33: high frequency 761441494, total 3470405430, capacity 4886513434. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 34: high frequency 765162430, total 3509701152, capacity 4943408951. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 35: high frequency 768852504, total 3547785602, capacity 4998303664. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 36: high frequency 772356330, total 3582366192, capacity 5048477640. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 37: high frequency 775719563, total 3614117609, capacity 5094429592. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 93 Alignment candidates after lowhash iteration 38: high frequency 779393825, total 3654757279, capacity 5153036605. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 91 Alignment candidates after lowhash iteration 39: high frequency 782898300, total 3686131115, capacity 5198668702. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 40: high frequency 786560685, total 3718682081, capacity 5246130324. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 41: high frequency 790184321, total 3750335240, capacity 5292115193. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 42: high frequency 793639972, total 3779130737, capacity 5334160313. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 43: high frequency 797176823, total 3806727967, capacity 5374447241. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 44: high frequency 800688516, total 3833492787, capacity 5413024065. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 90 Alignment candidates after lowhash iteration 45: high frequency 804013640, total 3858689875, capacity 5449759575. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 46: high frequency 807744893, total 3886080909, capacity 5489464553. Automatic settings for this iteration: minBucketSize 10, maxBucketSize 91 Alignment candidates after lowhash iteration 47: high frequency 811324886, total 3911033038, capacity 5525787665. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 48: high frequency 815053828, total 3936898416, capacity 5563569727. Automatic settings for this iteration: minBucketSize 9, maxBucketSize 92 Alignment candidates after lowhash iteration 49: high frequency 818824893, total 3962238572, capacity 5600133255. Found 818824893 alignment candidates. Average number of alignment candidates per oriented read is 65.0466. Number of alignment candidates before suppression is 818824893 Suppressed 0 alignment candidates. Number of alignment candidates after suppression is 818824893 2025-Jan-22 13:34:21.747748 Computing unique markers. 2025-Jan-22 13:36:56.579633 Alignment computation begins. 2025-Jan-22 14:25:56.186064 Alignment computation completed. Found and stored 384479556 good alignments. Keeping 278475711 alignments of 384479556 Flagged 6655 reads as chimeric out of 12588286 total. Chimera rate is 0.000528666 Kept 1548297774 disjoint sets with coverage in the requested range. Found 0 disjoint sets with more than one marker on a single oriented read or with less than 0 supporting oriented reads on each strand. Automatically set: minPrimaryCoverage = 7, maxPrimaryCoverage = 88 Found 952576568 primary marker graph edges. 2025-Jan-22 15:57:04.925725 Assembling connected component 0 of 300 This connected component has 24782628 oriented reads and 945559640 anchors. This connected component is self-complementary.