SPECIES = geoduck_roberts
OUTPUT_DIR = /home/ec2-user/PGTools/proximo/out/geoduck_roberts/
DRAFT_ASSEMBLY_FASTA = /home/ec2-user/PGScratch/geoduck_roberts/duck4-p.fasta
SAM_DIR = /home/ec2-user/PGScratch/geoduck_roberts
SAM_FILES = geoduck_roberts.bam
RE_SITE_SEQ = GATC
USE_REFERENCE = 0
SIM_BIN_SIZE = 50000
REF_ASSEMBLY_FASTA = None
BLAST_FILE_HEAD = None
DO_CLUSTERING = 1
DO_ORDERING   = 1
DO_REPORTING  = 1
OVERWRITE_GLM = 1
OVERWRITE_CLMS = 1
RANDOMIZE = 0
CLUSTER_N = 18
CLUSTER_CONTIGS_WITH_CENS = -1
CLUSTER_BANNED_CONTIG_MERGES = -1
CLUSTER_MIN_RE_SITES = 121
CLUSTER_MAX_LINK_DENSITY = 2.42210507848
CLUSTER_NONINFORMATIVE_RATIO = 2.18018057249
CLUSTER_DRAW_HEATMAP = 1
CLUSTER_DRAW_DOTPLOT = 1
ORDER_MIN_N_RES_IN_TRUNK = 28
ORDER_MIN_N_RES_IN_SHREDS = 1
ORDER_ESTIMATE_GAPS = 0
ORDER_DRAW_DOTPLOTS = 1
REPORT_EXCLUDED_GROUPS = -1
REPORT_QUALITY_FILTER = 100
REPORT_DRAW_HEATMAP = 1





Sat Apr 21 17:44:28 2018: ReportChart!

Info about input assembly:
DE NOVO ASSEMBLY, with no reference genome (less validation available)
Species: geoduck_roberts
N contigs:	315013		Total length:	2205550088		N50:	177022
N clusters (derived):	18
N non-singleton clusters:	18
N orderings found:	18


############################
#                          #
#    CLUSTERING METRICS    #
#                          #
############################


Number of contigs in clusters:	1407		(0.4466% of all contigs)
Length of contigs in clusters:	1144806063	(51.91% of all sequence length)

+----------+-----------+-------------+
|  CLUSTER | NUMBER OF |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   | 
+----------+-----------+-------------+
|      0   |      30   |    95477635 |
|      1   |      76   |    91759823 |
|      2   |     114   |    77244227 |
|      3   |     130   |    75429476 |
|      4   |      43   |    73562211 |
|      5   |     115   |    70784492 |
|      6   |      65   |    66567220 |
|      7   |      65   |    61724164 |
|      8   |     103   |    61498435 |
|      9   |      77   |    61387063 |
|     10   |      51   |    61358821 |
|     11   |     117   |    60960815 |
|     12   |      71   |    50036966 |
|     13   |      65   |    48895467 |
|     14   |      57   |    48800499 |
|     15   |      98   |    48199040 |
|     16   |      93   |    47740670 |
|     17   |      37   |    43379039 |
+----------+-----------+-------------+
|   TOTAL  |    1407   |  1144806063 |
+----------+-----------+-------------+


############################
#                          #
#     ORDERING METRICS     #
#                          #
############################



+----------+-----------+-------------+-------------+
| SCAFFOLD | NUMBER OF |  LENGTH OF  |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   |  SCAFFOLDS  |
+----------+-----------+-------------+-------------+
|      0   |      30   |    95477635 |    95477735 |
|      1   |      76   |    91759823 |    91759923 |
|      2   |     114   |    77244227 |    77244327 |
|      3   |     130   |    75429476 |    75429576 |
|      4   |      43   |    73562211 |    73562311 |
|      5   |     115   |    70784492 |    70784592 |
|      6   |      65   |    66567220 |    66567320 |
|      7   |      65   |    61724164 |    61724264 |
|      8   |     103   |    61498435 |    61498535 |
|      9   |      77   |    61387063 |    61387163 |
|     10   |      51   |    61358821 |    61358921 |
|     11   |     117   |    60960815 |    60960915 |
|     12   |      71   |    50036966 |    50037066 |
|     13   |      65   |    48895467 |    48895567 |
|     14   |      57   |    48800499 |    48800599 |
|     15   |      98   |    48199040 |    48199140 |
|     16   |      93   |    47740670 |    47740770 |
|     17   |      37   |    43379039 |    43379139 |
+----------+-----------+-------------+-------------+
|   TOTAL  |      18   |  1144806063 |  1144807863 |
+----------+-----------+-------------+-------------+

Number of contigs in scaffolds:			1407		(100% of all contigs in chromosome clusters, 0.4466% of all contigs)
Length of contigs in scaffolds:			1144806063	(100% of all length in chromosome clusters, 51.91% of all sequence length)
Number of contigs in preliminary orderings:	468		(33.26% of contigs in scaffolds)
Length of contigs in preliminary orderings:	288467697	(25.2% of length in scaffolds)

Fraction of all contigs with high-differential log-likelihood:	955 (0.3032%), with length 1065438931 (48.31%)
Fraction of scaffolded contigs with high-differential log-likelihood:	955 (67.87%), with length 1065438931 (93.07%)
Fraction of contigs in preliminary orderings with high-differential log-likelihood:	303 (64.74%), with length 267276024 (92.65%)