SPECIES = geoduck_roberts_zk
OUTPUT_DIR = /home/ec2-user/PGTools/proximo/out/geoduck_roberts_zk/
DRAFT_ASSEMBLY_FASTA = /home/ec2-user/PGScratch/geoduck_roberts_zk/duck4-p.fasta
SAM_DIR = /home/ec2-user/PGScratch/geoduck_roberts_zk
SAM_FILES = geoduck_roberts_zk.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 = 20
CLUSTER_MAX_LINK_DENSITY = 2.41675573632
CLUSTER_NONINFORMATIVE_RATIO = 1.27760723178
CLUSTER_DRAW_HEATMAP = 1
CLUSTER_DRAW_DOTPLOT = 1
ORDER_MIN_N_RES_IN_TRUNK = 40
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





Thu Aug  9 07:47:18 2018: ReportChart!

Info about input assembly:
DE NOVO ASSEMBLY, with no reference genome (less validation available)
Species: geoduck_roberts_zk
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:	24203		(7.683% of all contigs)
Length of contigs in clusters:	1423311825	(64.53% of all sequence length)

+----------+-----------+-------------+
|  CLUSTER | NUMBER OF |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   | 
+----------+-----------+-------------+
|      0   |    2210   |   142893309 |
|      1   |    1795   |   136856070 |
|      2   |    2188   |   121303014 |
|      3   |     887   |   117962894 |
|      4   |    1660   |   114223051 |
|      5   |    2520   |   113915087 |
|      6   |    1415   |    91541931 |
|      7   |    1719   |    90582098 |
|      8   |    1221   |    72702724 |
|      9   |    1202   |    71928283 |
|     10   |    1224   |    67859217 |
|     11   |    1683   |    64564079 |
|     12   |     881   |    61225558 |
|     13   |    1057   |    56965816 |
|     14   |     993   |    39767167 |
|     15   |     958   |    35539390 |
|     16   |     583   |    21402341 |
|     17   |       7   |     2079796 |
+----------+-----------+-------------+
|   TOTAL  |   24203   |  1423311825 |
+----------+-----------+-------------+


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



+----------+-----------+-------------+-------------+
| SCAFFOLD | NUMBER OF |  LENGTH OF  |  LENGTH OF  |
|  NUMBER  |  CONTIGS  |   CONTIGS   |  SCAFFOLDS  |
+----------+-----------+-------------+-------------+
|      0   |    2210   |   142893309 |   142893409 |
|      1   |    1795   |   136856070 |   136856170 |
|      2   |    2188   |   121303014 |   121303114 |
|      3   |     887   |   117962894 |   117962994 |
|      4   |    1660   |   114223051 |   114223151 |
|      5   |    2520   |   113915087 |   113915187 |
|      6   |    1415   |    91541931 |    91542031 |
|      7   |    1719   |    90582098 |    90582198 |
|      8   |    1221   |    72702724 |    72702824 |
|      9   |    1202   |    71928283 |    71928383 |
|     10   |    1224   |    67859217 |    67859317 |
|     11   |    1683   |    64564079 |    64564179 |
|     12   |     881   |    61225558 |    61225658 |
|     13   |    1057   |    56965816 |    56965916 |
|     14   |     993   |    39767167 |    39767267 |
|     15   |     958   |    35539390 |    35539490 |
|     16   |     583   |    21402341 |    21402441 |
|     17   |       7   |     2079796 |     2079896 |
+----------+-----------+-------------+-------------+
|   TOTAL  |      18   |  1423311825 |  1423313625 |
+----------+-----------+-------------+-------------+

Number of contigs in scaffolds:			24203		(100% of all contigs in chromosome clusters, 7.683% of all contigs)
Length of contigs in scaffolds:			1423311825	(100% of all length in chromosome clusters, 64.53% of all sequence length)
Number of contigs in preliminary orderings:	813		(3.359% of contigs in scaffolds)
Length of contigs in preliminary orderings:	121466104	(8.534% of length in scaffolds)

Fraction of all contigs with high-differential log-likelihood:	3106 (0.986%), with length 728150265 (33.01%)
Fraction of scaffolded contigs with high-differential log-likelihood:	3106 (12.83%), with length 728150265 (51.16%)
Fraction of contigs in preliminary orderings with high-differential log-likelihood:	202 (24.85%), with length 94752735 (78.01%)