Bugs

[GaryEBenson]

Bug:
If an index file is empty, step 2 will fail.
These files have to be manually deleted.

Error in step1:
Starting id must be greater than or equal to 1. Aborting.
No startng id provided. Aborting.
Usage: trf2proclu-ngs.exe -f -m -s -i -o -p -l [input.dat]
Where:
-f specifies the id assigned to the first record in the file (must be greater than or equal to 1),
-m must be equal to the matching weight parameter of the corresponding TRF run,
-s must be equal to the mismatch penalty parameter of the corresponding TRF run,
-i must be equal to the indel penalty parameter of the corresponding TRF run,
-o specifies the prefix of the output files,
-p specifies minimum patsize to keep TR,
-l specifies minimum flanksize (either side) to keep TR
trf2proclu-ngs.exe reads a DAT file output by the TRF and produces an LEB36 file and an index file that contains records from the DAT file each preceded by a unique id.

Error 8:
DBD::SQLite::st execute_array failed: UNIQUE constraint failed: fasta_reads.sid [err was 19 now 2000000000]
executing 100000 generated 67335 errors at /projectnb/vntrseek/marzie/human_vntrs/new_genomes/vntrseek1.10.0-rc.4/lib/vutil.pm line 1335, <$r_fh>
line 8304.

UNIQUE constraint failed: fasta_reads.sid (rows: 17300,17306-17307,17313,17334-17335,17344,17349,17354,17360,17374,17380,17390,17397,17406,17423,
17434,17443,17450,17452,17455,17457,17463,17470,17474,17483,17493,17512,17515-17516,17527,17530,17554,17557,17559,17561-17562,17565-17566,17571,1
7573-17574,17583,17587,17603,17607,17611,17615,17627,17633,17645,17648,17654,17657,17664,17691,17700,17711,17713,17741,17756,17771-17772,17776,17
784-17785,17810,17821,17830-17831,17843,17860,17869,17872,17879,17890-17891,17894,17898,17911-17912,17922-17923,17930,17940-17941,17944,17946-179
47,17949,17957,17965-17966,17968-17969,17977-17978,17981,17984,17986,17988-17989,17999,18001,18004,18033,18040,18046,18055,18071,18087,18089,1809
6-18097,18104,18108,18113,18119,18121,18127-18128,18130,18132,18138-18139,18149,18164-18165,18175,18177,18186,18193,18196,18203,18207,18210,18216
-18217,18222,18234,18244,18247-18248,18259,18262,18264,18266,18276,18279,18290,18295,18299,18306,18320,18331,18337-18338,18351,18373,18376,18378-
18379,18384-18385,18398,18407,18421,18448,18455,18457,18464,18466,18468,18473,18502,18504,18507,18509,18530,18535-18536,18539,18544,18546,18549,1
8552,18554,18560,18565,18567,18575-18576,18589,18591,18595,18597-18598,18600,18618,18626,18644,18652,18663,18681,18692,18719,18723,18725-18726,18
746-18747,18751,18758,18765,18768,18783,18787,18791,18796,18803,18806,18813,18821,18824-18825,18831,18833,18850,18854,18864-18865,18878,18882,188
87-18888,18890,18897,18911,18913,18915,18917,18919-18920,18923-18924,18927,18935,18937,18942,18955-18956,18964,18979,18983,18985-18986,18994,1899
9,19001-19002,19022,19024,19037-19038,19041,19049,19078,19084,19088,19098-19099,19108,19110,19127,19132,19135,19139,19157,19159-19161,19189,19193
,19200,19203,19206,19211,19214,19217-19218,19223,19227,19231,19241,19257,19259,19271,19298,19307-19308,19310,19326-19327,19334,19342,19347,19349,
19360,19364,19375,19403-19404,19410-19411,19425,19431,19433,19443,19455,19465-19466,19470,19475,19477,19488,19494,19499,19502-19503,19531,19536-1
9537,19543,19550-19551,19554,19564,19566,19584,19587,19595,19599-19600,19606,19613,19615-19616,19619,19624,19634,19653,19656,19673,19675,19684,19
692,19702,19705,19712,19717,19725,19734,19737,19748,19758,19763,19782,19793,19797,19812,19817,19821,19858,19862,19871-19872,19901,19903-19904,199
09,19911,19925,19930,19941,19943,19946,19948,19950,19953-19954,19957,19970,19974-19975,19987,20000,20002,20005,20015,20032,20041,20065,20068,2007
1,20082,20102,20107,20122,20128,20132,20142,20156,20190,20195,20199,20203,20209,20213,20218,20225,20239,20243,20245,20252-20253,20256,20261,20266
,20276,20281,20286,20290,20296,20302-20303,20323,20345-20346,20350,20356,20359,20381,20386,20393,20396,20410,20415,20427-20428,20430,20437,20444,
20448-20449,20454,20472,20489,20496,20503,20506,20511,20520,20527,20531,20533-20534,20546,20558,20571,20599,20602,20634,20644,20656,20669,20672,2
0706-20707,20716,20722-20723,20728-20729,20731,20734,20737,20751,20757,20759,20766,20769-20770,20776,20781,20791,20793,20809,20812,20840-20841,20
849,20851,20853-20855,20862-20865,20874,20890,20893,20909,20917,20933,20946,20949,20954,20964,20977,20990-20991,20997,21000,21004,21015,21017,210
30,21049,21068,21072,21075,21094-21096,21116,21124,21131,21149,21154-21155,21166-21167,21169,21173-21174,21177,21181,21183,21191,21195,21201,2120
3,21211,21214,21227,21232,21238,21240,21258,21260,21268,21277,21284,21291,21295-21296,21301,21313,21321-21323,21327,21350,21353,21362,21364,21367
-21369,21380,21382-21383,21386,21392,21413,21418,21420,21427-21429,21437,21439,21456,21461,21463,21472,21478,21494,21500,21503,21510-21512,21517,
21521-21522,21526,21529,21535,21537,21545,21549,21551,21557,21567,21576,21591,21597,21620,21633,21644,21646,21667,21669,21674,21679,21685,21714,2
1716,21724-21725,21737,21740-21741,21746,21750,21758-21760,21766,21787,21790-21791,21796,21810-21811,21818,21846,21885,21889,21891,21897-21898,21
912-21913,21918,21924,21928-21929,21934-21936,21938-21939,21941,21949,21962,21978,21987,21993,22003,22006,22008-22009,22011,22013,22024,22030,220
39,22042,22050,22052,22054-22055,22060,22080,22092,22101,22107,22128,22130,22140,22159,22166-22167,22169,22172-22173,22184,22192,22197,22209,2221
4,22216,22221,22225,22236,22254,22258-22259,22274-22275,22277-22278,22290,22300,22307,22338,22341,22348,22363,22365,22368,22370,22380,22388,22414
,22416,22418,22420,22425,22427,22441,22448,22457,22466,22468-22469,22471,22488,22501,22512,22524,22532-22534,22536,22540,22544,22551,22556,22559,
22561,22574,22576,22579,22584,22592,22608,22615-22616,22619,22636,28088-82012,87354-99999)
Error inserting reads. row dump: $VAR1 = [
[
2845022,
'A00404:45:HFKT7DSXX:3:2528:7066:17675 2:N:0:CATAGAGT+TGCCACCA',
'CATTCTTAAGAATGAATAAATAGAGAAAAGTGGCAGTAGAGAGTCATGCTTTTTAGAAAATAAAAATGCAGAGAATAAAAATGCTGCCCTTGCCAAAAATGTCTTCATTCCTTCAACTTTTCATGAATTAAA
GAATCATTGCATTTCTTC'
],
[
2845943,
'A00404:45:HFKT7DSXX:3:2522:3947:17221 2:N:0:CATAGAGT+TGCCACCA',
'TATCGTAAAAAGTAGAGAGGTAGGTAGCTTCCAATGATCTTGTGCTTCCAATGATTCTGTACTTCCAAAAGAAGGACAGCTATTAAAAGCACCATGTCTTCATGTCCCATATGGTGTATTTACTAAACTCAA
TTAAATTTTTAAAAAATA'
],
[
2846903,
'A00404:45:HFKT7DSXX:3:2522:14443:21746 2:N:0:CATAGAGT+TGCCACCA',
'AAGAAATTTTAAAAATATCCTATTAACTCCTGAGTAAAAGGAAAAATATAAACAGAAAATACATATGTTTAAATATGTAAATACATATTTTGTATGTAAATATGTTTTTCTATGCAAATATATATTTACATA
TTATTTTAAAATATACAA'
],