From: Langhorst, B. <Lan...@ne...> - 2015-03-22 21:41:26
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Hi: My frag store has finally been built, but runCA can’t continue because it can’t figure out the number of frags in the store. Is it normal for the endIID to be < 0? gatekeeper -lastfragiid deer.gkpStore Last frag in store is iid = -392887142 runCA can’t handle that. in getNumberOfFragsInStore, this regex fails to match due to the “-" $numFrags = $1 if (m/^Last frag in store is iid = (\d+)$/); I could fix that, but it doesn’t seem very reasonable to report a negative value from a function that is supposed to be counting the number of frags in a store. Should I fix the getNumberOfFragsInStore function to just parse this file and return the “active” column? or is this an indication of some deeper problem? Where should I look next? Thanks, Brad Here is the .info file: libIID bgnIID endIID active deleted mated totLen clrLen libName 0 1 -392887142 3902080154 0 3902080154 589214103254 589214103254 GLOBAL 0 0 0 0 0 0 0 0 LegacyUnmatedReads 1 1 1321836050 1321836050 0 1321836050 199597243550 199597243550 run15 2 1321836051 2564548948 1242712898 0 1242712898 187649647598 187649647598 run16 3 2564548949 3902080154 1337531206 0 1337531206 201967212106 201967212106 run17 -- Brad Langhorst, Ph.D. Applications and Product Development Scientist |