bolosky
commented
9 years ago I should know better than ever to have a constant-sized buffer for anything.
I’ll fix it soon.
--Bill
From: Richard Smith-Unna [mailto:notifications@github.com] Sent: Friday, October 16, 2015 6:50 AM To: amplab/snap snap@noreply.github.com Subject: [snap] Very long FASTA defline parsed incorrectly, crashes (#60)
FASTA file contained a character that's not a valid base (or N): '1', full line '10683, 10693, 10428, 10327, 10211, 10426, 10325, 10514, 10425, 10324, 10599, 10569, 10670, 10512, 10422, 10320, 10203, 9963, 9964, -2]';
converting to 'N'. This may happen again, but there will be no more warnings.
Saving genome...1s
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
This comes from a very long FASTA header in the assembly, but there's no newline in either of the two headers that contain this string. The two headers are included below:
TR24039_c0_g1_i1 len=6045 path=[10023:0-283 10024:284-289 10025:290-307 10620:308-313 10598:314-334 10568:335-367 @10420@!:368-463 10510:464-514 10038:515-520 10419:521-737 9752:738-775 10315:776-798 10509:799-885 10418:886-889 10313:890-913 9908:914-919 10416:920-948 10508:949-1018 10312:1019-1042 10415:1043-1073 9503:1074-1097 10597:1098-1295 10659:1296-1303 10566:1304-1319 10619:1320-1327 10596:1328-1336 10564:1337-1392 10306:1393-1394 10631:1395-1397 10618:1398-1416 10595:1417-1442 10660:1443-1466 10674:1467-1480 10303:1481-1527 9663:1528-1528 9664:1529-1562 10406:1563-1696 9710:1697-1777 10562:1778-1858 9394:1859-1883 10405:1884-1987 10499:1988-2032 10594:2033-2039 10561:2040-2063 10498:2064-2064 10403:2065-2088 10298:2089-2173 9510:2174-2197 10560:2198-2306 10297:2307-2389 10593:2390-2434 10661:2435-2458 10675:2459-2471 10295:2472-2500 10494:2501-2518 10399:2519-2542 10293:2543-2593 10493:2594-2617 10398:2618-2647 10292:2648-2671 10492:2672-2704 9422:2705
-2728 10
397:2729-3027 10662:3028-3051 10676:3052-3061 10687:3062-3085 10697:3086-3113 10490:3114-3139 10395:3140-3150 10558:3151-3175 10488:3176-3202 10393:3203-3206 10286:3207-3213 10486:3214-3237 10391:3238-3240 10663:3241-3247 10677:3248-3278 9892:3279-3318 10554:3319-3371 10481:3372-3395 10386:3396-3419 10280:3420-3464 10552:3465-3488 10480:3489-3490 10385:3491-3514 10613:3515-3545 10587:3546-3569 10551:3570-3661 10664:3662-3668 10276:3669-3685 10645:3686-3686 10636:3687-3692 10626:3693-3693 10612:3694-3710 10586:3711-3718 10549:3719-3722 10472:3723-3746 10635:3747-3772 10611:3773-3796 10625:3797-3799 10546:3800-3823 10610:3824-3856 10469:3857-3869 10261:3870-3901 10371:3902-3937 10583:3938-3961 10467:3962-4009 10544:4010-4033 10665:4034-4045 10679:4046-4069 10689:4070-4070 10256:4071-4105 10643:4106-4139 10624:4140-4161 10608:4162-4180 10581:4181-4189 10360:4190-4213 10535:4214-4243 10248:4244-4267 10454:4268-4293 10534:4294-4315 10358:4316-4339 10623:4340-4378 10607:4379-4402
10580:44
03-4498 10452:4499-4522 10356:4523-4525 10244:4526-4543 10532:4544-4546 10449:4547-4582 10353:4583-4585 10530:4586-4621 10718:4622-4639 10713:4640-4663 10707:4664-4682 10237:4683-4726 9991:4727-4727 9992:4728-4751 10444:4752-4759 10347:4760-4766 10234:4767-4801 9644:4802-4823 9645:4824-4847 9646:4848-4849 10440:4850-4918 10730:4919-4927 10343:4928-4966 10712:4967-4990 10228:4991-5044 10632:5045-5078 10603:5079-5110 10574:5111-5138 10520:5139-5167 10602:5168-5170 10573:5171-5218 10335:5219-5242 10518:5243-5274 10433:5275-5298 10601:5299-5335 10571:5336-5359 10517:5360-5398 10331:5399-5443 10600:5444-5467 10570:5468-5539 10669:5540-5542 10515:5543-5563 10683:5564-5566 10693:5567-5632 10428:5633-5645 10327:5646-5669 10211:5670-5674 10426:5675-5692 10325:5693-5716 10514:5717-5717 10425:5718-5741 10324:5742-5761 10599:5762-5800 10569:5801-5824 10670:5825-5827 10512:5828-5872 10422:5873-5908 10320:5909-5959 10203:5960-5999 9963:6000-6023 9964:6024-6044] [-1, 10023, 10024, 10025, 1
0620, 10
598, 10568, 10420, 10510, 10038, 10419, 9752, 10315, 10509, 10418, 10313, 9908, 10416, 10508, 10312, 10415, 9503, 10597, 10659, 10566, 10619, 10596, 10564, 10306, 10631, 10618, 10595, 10660, 10674, 10303, 9663, 9664, 10406, 9710, 10562, 9394, 10405, 10499, 10594, 10561, 10498, 10403, 10298, 9510, 10560, 10297, 10593, 10661, 10675, 10295, 10494, 10399, 10293, 10493, 10398, 10292, 10492, 9422, 10397, 10662, 10676, 10687, 10697, 10490, 10395, 10558, 10488, 10393, 10286, 10486, 10391, 10663, 10677, 9892, 10554, 10481, 10386, 10280, 10552, 10480, 10385, 10613, 10587, 10551, 10664, 10276, 10645, 10636, 10626, 10612, 10586, 10549, 10472, 10635, 10611, 10625, 10546, 10610, 10469, 10261, 10371, 10583, 10467, 10544, 10665, 10679, 10689, 10256, 10643, 10624, 10608, 10581, 10360, 10535, 10248, 10454, 10534, 10358, 10623, 10607, 10580, 10452, 10356, 10244, 10532, 10449, 10353, 10530, 10718, 10713, 10707, 10237, 9991, 9992, 10444, 10347, 10234, 9644, 9645, 9646, 10440, 10730, 10343, 10712
, 10228,
10632, 10603, 10574, 10520, 10602, 10573, 10335, 10518, 10433, 10601, 10571, 10517, 10331, 10600, 10570, 10669, 10515, 10683, 10693, 10428, 10327, 10211, 10426, 10325, 10514, 10425, 10324, 10599, 10569, 10670, 10512, 10422, 10320, 10203, 9963, 9964, -2]
TR24039_c0_g1_i2 len=6013 path=[9298:0-283 10421:284-307 10620:308-313 10598:314-334 10568:335-367 @10420@!:368-463 10510:464-514 10038:515-520 10419:521-737 9752:738-775 10315:776-798 10509:799-885 10418:886-889 10313:890-913 9908:914-919 10416:920-948 10508:949-1018 10312:1019-1042 10415:1043-1073 9503:1074-1097 10597:1098-1295 10659:1296-1303 10413:1304-1327 10565:1328-1336 10505:1337-1397 10618:1398-1416 10595:1417-1442 10660:1443-1466 10674:1467-1480 10303:1481-1527 9663:1528-1528 9664:1529-1562 10406:1563-1696 9710:1697-1777 10562:1778-1858 9394:1859-1883 10405:1884-1987 10499:1988-2032 10594:2033-2039 10561:2040-2063 10498:2064-2064 10403:2065-2088 10298:2089-2173 9510:2174-2197 10560:2198-2306 10297:2307-2389 10593:2390-2434 10661:2435-2458 10675:2459-2471 10295:2472-2500 10494:2501-2518 10399:2519-2542 10293:2543-2593 10493:2594-2617 10398:2618-2647 10292:2648-2671 10492:2672-2704 9422:2705-2728 10397:2729-3027 10662:3028-3051 10676:3052-3061 10687:3062-3085 1069
7:3086-3
113 10489:3114-3139 10394:3140-3150 10287:3151-3175 10487:3176-3202 10592:3203-3240 10557:3241-3247 10485:3248-3278 10390:3279-3318 10553:3319-3371 10481:3372-3395 10386:3396-3419 10280:3420-3464 10552:3465-3488 10480:3489-3490 10385:3491-3514 10613:3515-3545 10587:3546-3569 10551:3570-3661 9796:3662-3685 10645:3686-3686 10636:3687-3692 10626:3693-3693 10612:3694-3710 10586:3711-3718 10549:3719-3722 10472:3723-3746 10635:3747-3772 10611:3773-3796 10625:3797-3799 10546:3800-3823 10610:3824-3856 10469:3857-3869 10261:3870-3901 10371:3902-3937 10583:3938-3961 10467:3962-4009 10544:4010-4033 10665:4034-4045 10679:4046-4069 10689:4070-4070 10256:4071-4105 10643:4106-4139 10624:4140-4161 10608:4162-4180 10581:4181-4189 10360:4190-4213 10535:4214-4243 10248:4244-4267 10454:4268-4293 10534:4294-4315 10358:4316-4339 10623:4340-4378 10607:4379-4402 10580:4403-4498 10452:4499-4522 10356:4523-4525 10244:4526-4543 10532:4544-4546 10449:4547-4582 10353:4583-4585 10530:4586-4621 10718:4622
-4639 10
713:4640-4663 10707:4664-4682 10237:4683-4726 9991:4727-4727 9992:4728-4751 10444:4752-4759 10347:4760-4766 10234:4767-4801 9644:4802-4823 9645:4824-4847 9646:4848-4849 10440:4850-4918 10730:4919-4927 10343:4928-4966 10712:4967-4990 10228:4991-5044 10632:5045-5078 10603:5079-5110 10574:5111-5138 10520:5139-5167 10602:5168-5170 10573:5171-5218 10335:5219-5242 10518:5243-5274 10433:5275-5298 10601:5299-5335 10571:5336-5359 10517:5360-5398 10331:5399-5443 10600:5444-5467 10570:5468-5539 10669:5540-5542 10515:5543-5563 10683:5564-5566 10693:5567-5632 10428:5633-5645 10327:5646-5669 10211:5670-5674 10426:5675-5692 10325:5693-5716 10514:5717-5717 10425:5718-5741 10324:5742-5761 10599:5762-5800 10569:5801-5824 10670:5825-5827 10321:5828-5872 10204:5873-5908 9522:5909-5972 9523:5973-6012] [-1, 9298, 10421, 10620, 10598, 10568, 10420, 10510, 10038, 10419, 9752, 10315, 10509, 10418, 10313, 9908, 10416, 10508, 10312, 10415, 9503, 10597, 10659, 10413, 10565, 10505, 10618, 10595, 10660,
10674, 1
0303, 9663, 9664, 10406, 9710, 10562, 9394, 10405, 10499, 10594, 10561, 10498, 10403, 10298, 9510, 10560, 10297, 10593, 10661, 10675, 10295, 10494, 10399, 10293, 10493, 10398, 10292, 10492, 9422, 10397, 10662, 10676, 10687, 10697, 10489, 10394, 10287, 10487, 10592, 10557, 10485, 10390, 10553, 10481, 10386, 10280, 10552, 10480, 10385, 10613, 10587, 10551, 9796, 10645, 10636, 10626, 10612, 10586, 10549, 10472, 10635, 10611, 10625, 10546, 10610, 10469, 10261, 10371, 10583, 10467, 10544, 10665, 10679, 10689, 10256, 10643, 10624, 10608, 10581, 10360, 10535, 10248, 10454, 10534, 10358, 10623, 10607, 10580, 10452, 10356, 10244, 10532, 10449, 10353, 10530, 10718, 10713, 10707, 10237, 9991, 9992, 10444, 10347, 10234, 9644, 9645, 9646, 10440, 10730, 10343, 10712, 10228, 10632, 10603, 10574, 10520, 10602, 10573, 10335, 10518, 10433, 10601, 10571, 10517, 10331, 10600, 10570, 10669, 10515, 10683, 10693, 10428, 10327, 10211, 10426, 10325, 10514, 10425, 10324, 10599, 10569, 10670, 10321, 1
0204, 95
22, 9523, -2]
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blahah
This comes from a very long FASTA header in the assembly, but there's no newline in either of the two headers that contain this string. The two headers are included below: