SPECIES = geoduck_roberts_filt
OUTPUT_DIR = /home/ec2-user/PGTools/proximo/out/geoduck_roberts_filt/
DRAFT_ASSEMBLY_FASTA = /home/ec2-user/PGScratch/geoduck_roberts_filt/duck4-p.fasta
SAM_DIR = /home/ec2-user/PGScratch/geoduck_roberts_filt
SAM_FILES = geoduck_roberts_filt.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 = 22
CLUSTER_MAX_LINK_DENSITY = 1.4669234007
CLUSTER_NONINFORMATIVE_RATIO = 1.44383722336
CLUSTER_DRAW_HEATMAP = 1
CLUSTER_DRAW_DOTPLOT = 1
ORDER_MIN_N_RES_IN_TRUNK = 797
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





Wed May  2 21:22:47 2018: ReportChart!

Info about input assembly:
DE NOVO ASSEMBLY, with no reference genome (less validation available)
Species: geoduck_roberts_filt
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:	6280		(1.994% of all contigs)
Length of contigs in clusters:	708392446	(32.12% of all sequence length)

+----------+-----------+-------------+
|  CLUSTER | NUMBER OF |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   | 
+----------+-----------+-------------+
|      0   |    6245   |   707986856 |
|      1   |       2   |       70212 |
|      2   |       2   |       46608 |
|      3   |       2   |       32642 |
|      4   |       2   |       32627 |
|      5   |       2   |       32164 |
|      6   |       2   |       27710 |
|      7   |       2   |       26736 |
|      8   |       2   |       25012 |
|      9   |       2   |       24376 |
|     10   |       2   |       21670 |
|     11   |       2   |       19862 |
|     12   |       2   |       19360 |
|     13   |       2   |        9779 |
|     14   |       3   |        7232 |
|     15   |       2   |        4139 |
|     16   |       2   |        2800 |
|     17   |       2   |        2661 |
+----------+-----------+-------------+
|   TOTAL  |    6280   |   708392446 |
+----------+-----------+-------------+


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



+----------+-----------+-------------+-------------+
| SCAFFOLD | NUMBER OF |  LENGTH OF  |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   |  SCAFFOLDS  |
+----------+-----------+-------------+-------------+
|      0   |    6245   |   707986856 |   707986956 |
|      1   |       2   |       70212 |       70312 |
|      2   |       2   |       46608 |       46708 |
|      3   |       2   |       32642 |       32742 |
|      4   |       2   |       32627 |       32727 |
|      5   |       2   |       32164 |       32264 |
|      6   |       2   |       27710 |       27810 |
|      7   |       2   |       26736 |       26836 |
|      8   |       2   |       25012 |       25112 |
|      9   |       2   |       24376 |       24476 |
|     10   |       2   |       21670 |       21770 |
|     11   |       2   |       19862 |       19962 |
|     12   |       2   |       19360 |       19460 |
|     13   |       2   |        9779 |        9879 |
|     14   |       3   |        7232 |        7332 |
|     15   |       2   |        4139 |        4239 |
|     16   |       2   |        2800 |        2900 |
|     17   |       2   |        2661 |        2761 |
+----------+-----------+-------------+-------------+
|   TOTAL  |      18   |   708392446 |   708394246 |
+----------+-----------+-------------+-------------+

Number of contigs in scaffolds:			6280		(100% of all contigs in chromosome clusters, 1.994% of all contigs)
Length of contigs in scaffolds:			708392446	(100% of all length in chromosome clusters, 32.12% of all sequence length)
Number of contigs in preliminary orderings:	70		(1.115% of contigs in scaffolds)
Length of contigs in preliminary orderings:	79354085	(11.2% of length in scaffolds)

Fraction of all contigs with high-differential log-likelihood:	391 (0.1241%), with length 308497071 (13.99%)
Fraction of scaffolded contigs with high-differential log-likelihood:	391 (6.226%), with length 308497071 (43.55%)
Fraction of contigs in preliminary orderings with high-differential log-likelihood:	20 (28.57%), with length 66656847 (84%)