PBSuite Documentation

Software for Long-Read Sequencing Data from PacBio

Brought to you by: acenglishbcm

JellyExample Output Notes

The Protocol.xml provided should produce a single scaffold as it's result.
You can check the output's stats by using summarizeAssembly.py jelly.out.fasta

====================
Scaffold Stats | withGaps | withoutGaps
====================
#Seqs  |       1
Min    |  48,505 |  48,505
1st Qu.|  48,505 |  48,505
Median |  48,505 |  48,505
Mean   |  48,505 |  48,505
3rd Qu.|  48,505 |  48,505
Max    |  48,505 |  48,505
Total  |  48,505 |  48,505
n50    |  48,505 |  48,505
n90    |  48,505 |  48,505
n95    |  48,505 |  48,505

====================
Contig Stats | withNs | withoutNs
====================
#Seqs  |       1
Min    |  48,505 |  48,505
1st Qu.|  48,505 |  48,505
Median |  48,505 |  48,505
Mean   |  48,505 |  48,505
3rd Qu.|  48,505 |  48,505
Max    |  48,505 |  48,505
Total  |  48,505 |  48,505
n50    |  48,505 |  48,505
n90    |  48,505 |  48,505
n95    |  48,505 |  48,505

====================
No Gaps!
====================
Non-gapped Ns Count:  0

The support stage's output (support/filtered_subreads.fastq.err) should look like:

Running Support.py mapping/filtered_subreads.fastq.m4 data/reference/lambda.gapInfo.bed support/filtered_subreads.fastq.gml
2014-08-12 15:09:44,564 [INFO] Building Helper Objects
2014-08-12 15:09:44,564 [INFO] Connecting Alignments
2014-08-12 15:09:44,675 [INFO] Classifying Alignments' Support
2014-08-12 15:09:44,716 [WARNING] Read ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/31986/662_3287'] self-extends Node ref0000003e5 Possible Evidence of Tandem Repeat on Singleton
2014-08-12 15:09:44,730 [WARNING] Read ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/15956/701_2749'] self-extends Node ref0000002e5 Possible Evidence of Tandem Repeat on Singleton
2014-08-12 15:09:44,752 [WARNING] Read ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/44067/1000_3246'] self-extends Node ref0000003e5 Possible Evidence of Tandem Repeat on Singleton
2014-08-12 15:09:44,759 [WARNING] Read ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/57008/1515_3578'] self-extends Node ref0000002e3 Possible Evidence of Tandem Repeat on Singleton
2014-08-12 15:09:44,768 [INFO] Saving Support Graph
2014-08-12 15:09:44,786 [INFO] Finished

assembly/extraction.err should look like

2014-08-12 15:15:33,300 [INFO] Running Extraction.py Protocol.xml
[WARNING] Couldn't find data/reference/lambda.qual... assuming there isn't a quality file for the reference
2014-08-12 15:15:33,301 [INFO] Opening GML Files
2014-08-12 15:15:33,361 [INFO] Loading Reference Sequence
2014-08-12 15:15:33,363 [INFO] Extracting Reads
2014-08-12 15:15:33,364 [INFO] Parsing data/reads/filtered_subreads.fastq
2014-08-12 15:15:33,391 [INFO] Loaded 500 Reads
2014-08-12 15:15:33,395 [INFO] Parsed 111 Reads
2014-08-12 15:15:33,468 [INFO] Finished

Any partciular gap's output (assembly/<gapName>/assembly.err) should look like

2014-08-12 15:16:41,083 [INFO] Running Assembly.py assembly/ref0000001.0e3_ref0000001.1e5 -p 50
2014-08-12 15:16:43,014 [INFO] Preunited 0 reads
2014-08-12 15:16:43,427 [INFO] Running Assembly.py assembly/ref0000001.0e3_ref0000001.1e5 -p 50
2014-08-12 15:16:43,429 [INFO] Extracting tails
2014-08-12 15:16:43,429 [INFO] Parsed 15 reads
2014-08-12 15:16:43,430 [INFO] Found 16 tails
2014-08-12 15:16:43,430 [INFO] 2 reads had double tails
2014-08-12 15:16:43,430 [INFO] Mapping Tails
2014-08-12 15:16:43,505 [INFO] [0, '[INFO] 2014-08-12T15:16:43 [blasr] started.\n[INFO] 2014-08-12T15:16:43 [blasr] ended.\n', None]
2014-08-12 15:16:43,505 [INFO] Consolidating alignments
2014-08-12 15:16:43,508 [INFO] 12 tails mapped
2014-08-12 15:16:43,513 [INFO] 9 reads span
2014-08-12 15:16:43,513 [INFO] 12 reads extend flank 1
2014-08-12 15:16:43,513 [INFO] 10 reads extend flank 2
2014-08-12 15:16:43,514 [INFO] estimated fill len 55
2014-08-12 15:16:43,516 [INFO] estimated flank 1 extend len 379
2014-08-12 15:16:43,520 [INFO] estimated flank 2 extend len 566
2014-08-12 15:16:43,567 [INFO] Cleaning 10 temp files
2014-08-12 15:16:43,578 [INFO] Finished

And output.err

2014-08-12 15:17:19,131 [INFO] Running /stornext/snfs5/next-gen/scratch/english/Jelly/DevJelly/trunk/bin/Collection.py /stornext/snfs5/next-gen/scratch/english/Jelly/DevJelly/trunk/docs/temp/Protocol.xml
2014-08-12 15:17:19,132 [INFO] Grabbing Filling Metrics
2014-08-12 15:17:19,136 [INFO] Number of Gaps Addressed 6
2014-08-12 15:17:19,136 [INFO] No Filling Metrics 0
2014-08-12 15:17:19,136 [INFO] Filled 6
2014-08-12 15:17:19,136 [INFO] NFilled 0
2014-08-12 15:17:19,136 [INFO] Single-End Reduced 0
2014-08-12 15:17:19,137 [INFO] Double-End Reduced 0
2014-08-12 15:17:19,137 [INFO] Overfilled 0
2014-08-12 15:17:19,137 [INFO] Gaps with trimmed edges 3
2014-08-12 15:17:19,137 [INFO] Loading Reference
2014-08-12 15:17:19,140 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/153813/407_2743', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/83004/1275_3380', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/102972/0_3833', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/47729/0_2244', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/102185/2437_4574', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/62059/3877_6525'] extends ref0000002.0e3
2014-08-12 15:17:19,140 [DEBUG] ref0000002.0e3
2014-08-12 15:17:19,140 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/127034/1244_4019'] extends ref0000001e5
2014-08-12 15:17:19,140 [DEBUG] ref0000001e5
2014-08-12 15:17:19,140 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/10010/2586_4779', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/115576/101_2217'] extends ref0000001e3
2014-08-12 15:17:19,140 [DEBUG] ref0000001e3
2014-08-12 15:17:19,140 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/132890/632_2868', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/7397/0_2338'] extends ref0000001.0e3
2014-08-12 15:17:19,140 [DEBUG] ref0000001.0e3
2014-08-12 15:17:19,141 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/16137/1121_4068', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/71504/2766_5060', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/15956/701_2749', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/77165/1985_4120', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/1264/2015_4029'] extends ref0000002e5
2014-08-12 15:17:19,141 [DEBUG] ref0000002e5
2014-08-12 15:17:19,141 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/106293/6545_8886', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/12522/1279_4200', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/76650/724_3068', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/141976/3194_6488', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/101540/2736_6169', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/57008/1515_3578'] extends ref0000002e3
2014-08-12 15:17:19,141 [DEBUG] ref0000002e3
2014-08-12 15:17:19,141 [DEBUG] ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/129135/2871_6130', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/31585/92_2548'] extends ref0000001.2e5
2014-08-12 15:17:19,141 [DEBUG] ref0000001.2e5
2014-08-12 15:17:19,141 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/4975/361_2594', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/130868/0_2054', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/139416/0_2012', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/15526/1205_3545', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/70457/1615_3717', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/34971/0_2390', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/103843/4788_7567', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/162444/882_4115'] extends ref0000002.1e5
2014-08-12 15:17:19,141 [DEBUG] ref0000002.1e5
2014-08-12 15:17:19,141 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/111657/312_2593', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/132241/4721_6905', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/74097/1836_3836', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/64061/1521_3706', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/58975/2394_4795', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/135782/55_2214', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/35540/2179_5756', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/39357/918_3248', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/113381/0_4133'] extends ref0000003e3
2014-08-12 15:17:19,142 [DEBUG] ref0000003e3
2014-08-12 15:17:19,142 [DEBUG] ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/31986/662_3287', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/44067/1000_3246'] extends ref0000003e5
2014-08-12 15:17:19,142 [DEBUG] ref0000003e5
2014-08-12 15:17:19,142 [DEBUG] ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/152611/265_2320', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/34189/3361_6179', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/117907/2824_4879', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/98815/57_2135', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/145929/1101_3110', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/27622/41_2086'] extends ref0000001.1e3
2014-08-12 15:17:19,142 [DEBUG] ref0000001.1e3
2014-08-12 15:17:19,142 [DEBUG] ['m130725_000747_00121_c100518582550000001823079209281362_s1_p0/4517/0_2609'] gives evidence ref0000002.0e3 -> ref0000002.1e5
2014-08-12 15:17:19,142 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/7845/1904_5089', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/126391/1940_5320', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/121280/1155_4486', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/141521/84_2329', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/101653/0_2122', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/91403/930_3363', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/136475/4312_6645', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/16723/1947_4121', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/134404/1582_5157', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/80471/0_2813', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/80452/2226_4391', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/71629/549_2861', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/134863/619_3249', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/134357/2559_5215', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/130161/0_3512', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/40504/882_3577', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/110107/281_2696', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/85185/3151_5492'] gives evidence ref0000001e5 -> ref0000002e3
2014-08-12 15:17:19,142 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/106927/275_2793', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/44505/3954_5995', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/116935/257_2331', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/82082/131_2318', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/70703/0_2025', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/95954/3296_6456', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/140712/0_2232', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/132195/2068_4169', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/131417/2215_4415', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/132195/0_2024', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/152690/1228_4037', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/139274/620_3273', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/131417/4463_6494', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/13375/2642_4706', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/43188/256_2281'] gives evidence ref0000001e3 -> ref0000003e5
2014-08-12 15:17:19,142 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/85104/0_4797', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/125169/0_2014', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/137877/4188_6226', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/51218/2185_4363', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/135956/843_3526', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/123470/877_2895', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/51218/2185_4363', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/6025/2824_5335', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/151031/333_2822', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/35277/900_3620', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/91683/1132_3306', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/4408/3659_5661', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/158766/2218_4783'] gives evidence ref0000001.0e3 -> ref0000001.1e5
2014-08-12 15:17:19,143 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/101035/2535_4607', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/54623/2486_4708', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/128971/2675_4926', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/106935/488_2976', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/11040/694_3147', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/147687/681_3024', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/153453/137_2402', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/134689/638_3007'] gives evidence ref0000002e5 -> ref0000003e3
2014-08-12 15:17:19,143 [DEBUG] ['m130724_230321_00121_c100518582550000001823079209281361_s1_p0/128458/2517_4587', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/63529/3525_6070', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/44084/1243_3408', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/122152/1676_4190', 'm130724_230321_00121_c100518582550000001823079209281361_s1_p0/93133/1602_4722', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/85821/4736_6931', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/88575/4565_6770', 'm130725_000747_00121_c100518582550000001823079209281362_s1_p0/101756/118_2433'] gives evidence ref0000001.2e5 -> ref0000001.1e3
2014-08-12 15:17:19,143 [INFO] Removing Poorly Supported Edges
2014-08-12 15:17:19,144 [INFO] PreFilter: 1 subGraphs
2014-08-12 15:17:19,146 [WARNING] Circular graph detected. Breaking weakest edge
2014-08-12 15:17:19,146 [DEBUG] HERE
2014-08-12 15:17:19,146 [DEBUG] ref0000001e5 ref0000002e3
2014-08-12 15:17:19,146 [DEBUG] 23
2014-08-12 15:17:19,146 [DEBUG] 5
2014-08-12 15:17:19,146 [DEBUG] HERE
2014-08-12 15:17:19,146 [DEBUG] ref0000001e3 ref0000003e5
2014-08-12 15:17:19,146 [DEBUG] 15
2014-08-12 15:17:19,146 [DEBUG] 4526
2014-08-12 15:17:19,146 [DEBUG] HERE
2014-08-12 15:17:19,146 [DEBUG] ref0000002e5 ref0000003e3
2014-08-12 15:17:19,147 [DEBUG] 8
2014-08-12 15:17:19,147 [DEBUG] 17594
2014-08-12 15:17:19,147 [INFO] breaking at ('ref0000001e5', 'ref0000002e3')
2014-08-12 15:17:19,147 [INFO] PostFilter: 1 subGraphs
2014-08-12 15:17:19,147 [INFO] Outputting new contigs
2014-08-12 15:17:19,150 [DEBUG] Contig 0
2014-08-12 15:17:19,150 [DEBUG] Moving from ref0000001e5 to ref0000001.0e3 (p=1)
2014-08-12 15:17:19,150 [DEBUG] contig
2014-08-12 15:17:19,150 [DEBUG] who? ref0000001e5 ref0000001.0e3
2014-08-12 15:17:19,151 [DEBUG] Grabbing contig between nodes ref0000001e5 & ref0000001.0e3 - [trim 0, 0]
2014-08-12 15:17:19,151 [DEBUG] contig 0 to 6004
2014-08-12 15:17:19,151 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,151 [DEBUG] Moving from ref0000001.0e3 to ref0000001.1e5 (p=1)
2014-08-12 15:17:19,151 [DEBUG] improved gap
2014-08-12 15:17:19,151 [DEBUG] Getting fill sequence for ref0000001.0e3_ref0000001.1e5
2014-08-12 15:17:19,151 [DEBUG] fill span
2014-08-12 15:17:19,151 [DEBUG] Moving from ref0000001.1e5 to ref0000001.1e3 (p=1)
2014-08-12 15:17:19,151 [DEBUG] contig
2014-08-12 15:17:19,152 [DEBUG] who? ref0000001.1e5 ref0000001.1e3
2014-08-12 15:17:19,152 [DEBUG] Grabbing contig between nodes ref0000001.1e5 & ref0000001.1e3 - [trim 0, 0]
2014-08-12 15:17:19,152 [DEBUG] contig 6054 to 10260
2014-08-12 15:17:19,152 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,152 [DEBUG] Moving from ref0000001.1e3 to ref0000001.2e5 (p=1)
2014-08-12 15:17:19,152 [DEBUG] improved gap
2014-08-12 15:17:19,152 [DEBUG] Getting fill sequence for ref0000001.1e3_ref0000001.2e5
2014-08-12 15:17:19,152 [DEBUG] fill span
2014-08-12 15:17:19,152 [DEBUG] Moving from ref0000001.2e5 to ref0000001e3 (p=1)
2014-08-12 15:17:19,152 [DEBUG] contig
2014-08-12 15:17:19,153 [DEBUG] who? ref0000001.2e5 ref0000001e3
2014-08-12 15:17:19,153 [DEBUG] Grabbing contig between nodes ref0000001.2e5 & ref0000001e3 - [trim 0, 0]
2014-08-12 15:17:19,153 [DEBUG] contig 10740 to 28380
2014-08-12 15:17:19,153 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,153 [DEBUG] Moving from ref0000001e3 to ref0000003e5 (p=1)
2014-08-12 15:17:19,153 [DEBUG] new sequence
2014-08-12 15:17:19,153 [DEBUG] Getting fill sequence for ref0000001e3_ref0000003e5
2014-08-12 15:17:19,153 [DEBUG] fill span
2014-08-12 15:17:19,153 [DEBUG] Moving from ref0000003e5 to ref0000003e3 (p=1)
2014-08-12 15:17:19,153 [DEBUG] contig
2014-08-12 15:17:19,154 [DEBUG] who? ref0000003e5 ref0000003e3
2014-08-12 15:17:19,154 [DEBUG] Grabbing contig between nodes ref0000003e5 & ref0000003e3 - [trim 0, 0]
2014-08-12 15:17:19,154 [DEBUG] contig 0 to 11219
2014-08-12 15:17:19,154 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,154 [DEBUG] Moving from ref0000003e3 to ref0000002e5 (p=1)
2014-08-12 15:17:19,154 [DEBUG] new sequence
2014-08-12 15:17:19,154 [DEBUG] Getting fill sequence for ref0000002e5_ref0000003e3
2014-08-12 15:17:19,154 [DEBUG] fill span
2014-08-12 15:17:19,154 [DEBUG] Moving from ref0000002e5 to ref0000002.0e3 (p=1)
2014-08-12 15:17:19,154 [DEBUG] contig
2014-08-12 15:17:19,154 [DEBUG] who? ref0000002e5 ref0000002.0e3
2014-08-12 15:17:19,155 [DEBUG] Grabbing contig between nodes ref0000002e5 & ref0000002.0e3 - [trim 0, 0]
2014-08-12 15:17:19,155 [DEBUG] contig 0 to 3240
2014-08-12 15:17:19,155 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,155 [DEBUG] Moving from ref0000002.0e3 to ref0000002.1e5 (p=1)
2014-08-12 15:17:19,155 [DEBUG] improved gap
2014-08-12 15:17:19,155 [DEBUG] Getting fill sequence for ref0000002.0e3_ref0000002.1e5
2014-08-12 15:17:19,155 [DEBUG] fill span
2014-08-12 15:17:19,155 [DEBUG] Moving from ref0000002.1e5 to ref0000002e3 (p=1)
2014-08-12 15:17:19,155 [DEBUG] contig
2014-08-12 15:17:19,155 [DEBUG] who? ref0000002.1e5 ref0000002e3
2014-08-12 15:17:19,156 [DEBUG] Grabbing contig between nodes ref0000002.1e5 & ref0000002e3 - [trim 0, 0]
2014-08-12 15:17:19,156 [DEBUG] contig 4201 to 8182
2014-08-12 15:17:19,156 [DEBUG] trimming 0 and 0
2014-08-12 15:17:19,160 [INFO] Finished!