varid exits and what does this error mean?

[urchgene]

Hi,

greetings................

First I must commend you guys for the very good softwares you are
making available for solid data analysis.

I have been using SHRiMP to map some reads to an EST build and now am
diving into VARiD to call the polymorphisms.

Please i get this error when i use samfiles generated from SHRiMP to
run VARiD........

<va_utils.c:339> assertion: (size!=0) failed, Last errno=2

see below:




TC33424:954 nt
TC33699:497 nt
TC34523:515 nt
TC35420:1093 nt
TC36136:588 nt
TC36353:880 nt
TC38890:1367 nt
TC39104:487 nt
TC40252:780 nt
TC40633:750 nt
TC12586:894 nt
TC13594:935 nt
TC15547:859 nt
TC17657:814 nt
TC18484:825 nt
TC19063:952 nt
TC19306:747 nt
TC19355:793 nt
TC20842:792 nt
TC21668:790 nt
TC21688:872 nt
TC22316:763 nt
TC24155:1125 nt
TC25349:820 nt
TC25759:2163 nt
TC27235:726 nt
TC27341:1397 nt
TC27852:862 nt
TC28903:918 nt
TC29363:706 nt
TC29506:1074 nt
TC29825:843 nt
TC30107:881 nt
TC30669:1515 nt
TC31436:642 nt
TC31746:712 nt
TC32211:1079 nt
TC32656:1449 nt
TC32707:1066 nt
TC33305:859 nt
TC35675:457 nt
TC37328:1018 nt
TC37897:662 nt
TC38277:1348 nt
TC38615:594 nt
TC39152:748 nt
TC40893:650 nt
TC12307:932 nt
TC12508:887 nt
TC12756:1066 nt
TC13131:876 nt
TC13387:923 nt
TC13620:1064 nt
TC14116:1049 nt
TC14327:1272 nt
TC15449:918 nt
TC15473:866 nt
TC15575:1694 nt
TC15586:915 nt
TC16720:793 nt
TC16749:852 nt
TC16828:848 nt
TC18801:981 nt
TC19768:1026 nt
TC19958:812 nt
TC20143:862 nt
TC20228:1390 nt
TC20830:993 nt
TC21729:1022 nt
TC21883:712 nt
TC22825:789 nt
TC23468:699 nt
TC23513:814 nt
TC24480:712 nt
TC24684:3328 nt
TC25324:780 nt
TC25369:653 nt
TC25407:670 nt
TC25514:1256 nt
TC25582:811 nt
TC25998:1706 nt
TC27493:1268 nt
TC27910:1419 nt
TC28329:883 nt
TC29253:840 nt
TC29802:957 nt
TC30181:737 nt
TC30650:881 nt
TC31125:891 nt
TC31385:1091 nt
TC32578:818 nt
TC34560:786 nt
TC34757:1576 nt
TC34902:606 nt
TC35219:812 nt
TC35445:1779 nt
TC35844:1403 nt
TC36185:738 nt
TC37076:1163 nt
TC37963:993 nt
TC39034:608 nt
TC39202:718 nt
TC39532:804 nt
TC39991:1282 nt
TC40351:1003 nt
TC40670:900 nt
TC40701:841 nt
TC40858:812 nt
TC41639:746 nt
TC41723:988 nt
TC41736:1220 nt
TC41820:1047 nt
S_K0000400003B09F1:105 nt
C_K0000400044D12F2:1228 nt
S_K0000100014H01F1:454 nt
S_K0000100006H11F1:620 nt
C_K0000400056E06F1:1847 nt
C_K0000400071B03F1:675 nt
S_K0000400071H07F1:615 nt
S_K0000100016C06F1:237 nt
S_K0000200001A05F1:277 nt
C_K0000100003C04F1:642 nt
S_K0000200008F06F1:461 nt
S_K0000100002D01F1:604 nt
C_K0000100017E12F1:524 nt
S_K0000400035G07F1:548 nt
S_K0000400064A10F1:619 nt
S_K0000200020D08F1:594 nt
S_K0000200019B10F1:513 nt
C_K0000200023G03F1:587 nt
S_K0000100013G06F1:628 nt
S_K0000200018D04F1:629 nt
C_K0000200023G09R1:545 nt
S_K0000100017A01F1:515 nt
C_K0000400050C02F1:575 nt
C_K0000200025B08F1:554 nt
S_K0000400063H06F1:514 nt
S_K0000100008C05F1:596 nt
S_K0000100010A02F1:239 nt
S_K0000200009D01F1:495 nt
C_K0000400013G02F1:511 nt
C_K0000400033E08F1:137 nt
S_K0000400028B09F1:187 nt
S_K0000100011D10F1:393 nt
S_K0000400002B10F1:549 nt
S_K0000200002D02F1:143 nt
C_K0000200020F01F1:453 nt
S_K0000400009G11F1:325 nt
S_K0000100010F04F1:516 nt
S_K0000400060B02F1:361 nt
S_K0000100019A08F1:357 nt
C_K0000400008C01F1:1700 nt
S_K0000400002G12F1:513 nt
S_K0000200021B03F1:336 nt
S_K0000400069B08F1:254 nt
S_K0000100005B03F1:333 nt
C_K0000400008H03F1:878 nt
S_K0000200028G04F1:330 nt
C_K0000100011H10F2:750 nt
S_K0000100014E01F1:599 nt
C_K0000400043C06F1:497 nt
S_K0000400048A11F1:438 nt
S_K0000200017C09F1:561 nt
S_K0000400041A12F1:97 nt
S_K0000200019G01F1:441 nt
C_K0000400047B03F1:633 nt
S_K0000200012G02F1:483 nt
S_K0000100002A01F1:543 nt
S_K0000400066A06F1:95 nt
C_K0000400034H05F1:590 nt
S_K0000200014B07F1:555 nt
C_K0000100016D06F1:571 nt
S_K0000100002F03F1:318 nt
S_K0000200027A07F1:407 nt
S_K0000400002G01F1:269 nt
S_K0000400058D11F1:389 nt
S_K0000200020A08F1:385 nt
S_K0000200027F09F2:568 nt
S_K0000100004A08F1:658 nt
C_K0000100007D03F1:717 nt
C_K0000100001B10F1:560 nt
S_K0000400072C02F1:465 nt
S_K0000200011A05F1:489 nt
C_K0000100013C04F1:593 nt
S_K0000400072H04F1:427 nt
C_K0000200005F04F1:521 nt
S_K0000400041F03F1:215 nt
S_K0000200024E07F1:273 nt
S_K0000100018F11F1:415 nt
S_K0000400010F09F1:263 nt
S_K0000400009D11F1:489 nt
S_K0000100010C04F1:480 nt
C_K0000400072G02F1:1067 nt
S_K0000100001E08F1:545 nt
S_K0000200002F04F1:290 nt
C_K0000100010B02F1:423 nt
S_K0000200015E04F1:497 nt
C_K0000100017G03F1:432 nt
S_K0000100014B01F1:557 nt
S_K0000200022B11F1:421 nt
S_K0000100006B11F1:270 nt
C_K0000100010G04F1:605 nt
C_K0000200015D02F1:512 nt
C_K0000400001E04F1:802 nt
S_K0000100014G03F1:483 nt
S_K0000400047E07F1:103 nt
S_K0000400006H11F1:405 nt
<va_utils.c:339> assertion: (size!=0) failed, Last errno=2
<run_wrap.c:781> ./varid_exec exiting...
<run_wrap.c:784> ./varid_exec exited

I cannot get a glimpse of what is wrong and how to approach this. I
will greatly appreciate your reply please.

Thank you.

[Misko Dzamba]

Hi,
Do you know which version of VARiD you are running? Can you by any
chance send some sample of the SAM file you are giving the program?
also can you please send the command you used to invoke VARiD for this
error to occur? Thanks,

Misko