Correction

Input Reads

/home/data/m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	52709 reads (184759902 bp)
FASTQ	13164 reads (7141400 bp) were short and not loaded
52709 reads (184759902 bp) loaded, 13164 reads (7141400 bp) skipped, 0 warnings
/home/data/m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	208699 reads (1410877678 bp)
FASTQ	11632 reads (6312452 bp) were short and not loaded
208699 reads (1410877678 bp) loaded, 11632 reads (6312452 bp) skipped, 0 warnings
/home/data/m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	181936 reads (1550559544 bp)
FASTQ	9316 reads (4927737 bp) were short and not loaded
181936 reads (1550559544 bp) loaded, 9316 reads (4927737 bp) skipped, 0 warnings
/home/data/m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	165045 reads (1410261808 bp)
FASTQ	8017 reads (4173674 bp) were short and not loaded
165045 reads (1410261808 bp) loaded, 8017 reads (4173674 bp) skipped, 0 warnings
/home/data/m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	179421 reads (1544932559 bp)
FASTQ	8817 reads (4619999 bp) were short and not loaded
179421 reads (1544932559 bp) loaded, 8817 reads (4619999 bp) skipped, 0 warnings
/home/data/m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	203941 reads (1464574518 bp)
FASTQ	12002 reads (6493337 bp) were short and not loaded
203941 reads (1464574518 bp) loaded, 12002 reads (6493337 bp) skipped, 0 warnings
/home/data/m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	205144 reads (1481891571 bp)
FASTQ	12089 reads (6445012 bp) were short and not loaded
205144 reads (1481891571 bp) loaded, 12089 reads (6445012 bp) skipped, 0 warnings
/home/data/m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	150624 reads (1034664090 bp)
FASTQ	8640 reads (4766921 bp) were short and not loaded
150624 reads (1034664090 bp) loaded, 8640 reads (4766921 bp) skipped, 0 warnings
/home/data/m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	134460 reads (911117475 bp)
FASTQ	8062 reads (4360929 bp) were short and not loaded
134460 reads (911117475 bp) loaded, 8062 reads (4360929 bp) skipped, 0 warnings
/home/data/m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	122547 reads (826646486 bp)
FASTQ	7462 reads (3971088 bp) were short and not loaded
122547 reads (826646486 bp) loaded, 7462 reads (3971088 bp) skipped, 0 warnings
/home/data/m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	0 reads (0 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	134326 reads (905373865 bp)
FASTQ	7737 reads (4217576 bp) were short and not loaded
134326 reads (905373865 bp) loaded, 7737 reads (4217576 bp) skipped, 0 warnings

Final Store

correction/20171018_oly_pacbio.gkpStore
readsLoaded	1738852 reads (12725659496 bp)
readsSkipped	106938 reads (57430125 bp) (read was too short)
warnings	0 warnings (invalid base or quality value)

Read Length Histogram

k-Mer Counts

Histogram for k=16 with 12699576716 mers, 1843464954 distinct mers and 385488671 single-copy mers. Largest count is 4763892.

Overlaps

Overlaps not computed.

Overlap Filtering

PARAMETERS
	40	expected coverage
	0	don't use overlaps shorter than this
	0.000	don't use overlaps with erate less than this
	1.000	don't use overlaps with erate more than this
OVERLAPS
Ignored	0	< 0.0000 fraction error
	0	> 0.4095 fraction error
	0	< 0 bases long
	0	> 2097151 bases long
Filtered	9033508064	too many overlaps, discard these shortest ones
Evidence	68112774	longest overlaps
Total	9101620838	all overlaps
READS
	874	no overlaps
	102785	no overlaps filtered
	111724	< 50% overlaps filtered
	303069	< 80% overlaps filtered
	629330	< 95% overlaps filtered
	1635193	< 100% overlaps filtered

Read Correction

Filter method: corFilter=expensive. Expect to correct 1737978 reads with bp to bp.

INPUTS
1737978	input reads
12703460519	input bases
OUTPUTS
72903	reads that failed to generate any corrected bases
1665075	corrected read pieces
11661226162	corrected bases
PIECES PER READ
0	72903
1	1665075

A single input read can be split into multiple output reads, or possibly not even output at all.

Scatter plot of the original read length (X axis) against the expected corrected read length (Y axis). Colors show a comparison of the simple filter (which doesn't use overlaps) to the expensive filter (which does). A large green triangle (false negatives) hints that there could be abnormally low quality regions in the reads.

Scatter plot of original vs expected read length. Shown in filter plot above.

Scatter plot of original vs corrected read length.

Scatter plot of expected vs corrected read length.

Histogram of the difference between the expected and corrected read lengths. Note that a negative difference means the corrected read is larger than expected.

Histogram of original (red), expected (green) and actual corrected (blue) read lengths.