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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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CIGAR/MD buffer not long enough #28

Closed dkainer closed 6 years ago

dkainer commented 7 years ago

I encountered the following error with some Nanopore long read data, using ngmlr v0.2.4:

CIGAR/MD buffer not long enough. Please report this! Warning: could not compute alignment for read 1cd31c83-45ed-4959-bba6-a65728b2209c Error in `ngmlr': free(): invalid next size (fast): 0x00007efcbc207080 ======= Backtrace: ========= [0x528f91] [0x531006] [0x534a27] [0x427a51] [0x41fd23] [0x41fecc] [0x423bb0] [0x4275f7] [0x434990] [0x434aa9] [0x414f4b] [0x41509b] [0x415b6d] [0x41cead] [0x41bd19] [0x44b825] [0x57c469] ======= Memory map: ======== 00400000-00659000 r-xp 00000000 203:acf3a 156035415797705592 /short/xf1/src_big/ngmlr-0.2.4/ngmlr 00859000-00863000 rw-p 00259000 203:acf3a 156035415797705592 /short/xf1/src_big/ngmlr-0.2.4/ngmlr 00863000-0086d000 rw-p 00000000 00:00 0 0148a000-018c8000 rw-p 00000000 00:00 0 [heap] 7efb31161000-7efbb0000000 rw-p 00000000 00:00 0 7efbb0000000-7efbb1926000 rw-p 00000000 00:00 0 7efbb1926000-7efbb4000000 ---p 00000000 00:00 0 7efbb43ab000-7efbd0000000 rw-p 00000000 00:00 0 7efbd0000000-7efbd2166000 rw-p 00000000 00:00 0 7efbd2166000-7efbd4000000 ---p 00000000 00:00 0 7efbd5f20000-7efbe5f21000 rw-p 00000000 00:00 0 7efbf609f000-7efc10000000 rw-p 00000000 00:00 0 7efc10000000-7efc1194b000 rw-p 00000000 00:00 0 7efc1194b000-7efc14000000 ---p 00000000 00:00 0 7efc15f23000-7efc2c000000 rw-p 00000000 00:00 0 7efc2c000000-7efc2cd01000 rw-p 00000000 00:00 0 7efc2cd01000-7efc30000000 ---p 00000000 00:00 0 7efc31f21000-7efc5c000000 rw-p 00000000 00:00 0 7efc5c000000-7efc5d4a0000 rw-p 00000000 00:00 0 7efc5d4a0000-7efc60000000 ---p 00000000 00:00 0 7efc61f21000-7efc75f23000 rw-p 00000000 00:00 0 7efc860a1000-7efc8c000000 rw-p 00000000 00:00 0 7efc8c000000-7efc8ce7c000 rw-p 00000000 00:00 0 7efc8ce7c000-7efc90000000 ---p 00000000 00:00 0 7efc91f21000-7efcbc000000 rw-p 00000000 00:00 0 7efcbc000000-7efcbd54d000 rw-p 00000000 00:00 0 7efcbd54d000-7efcc0000000 ---p 00000000 00:00 0 7efcc1f21000-7efcec000000 rw-p 00000000 00:00 0 7efcec000000-7efced020000 rw-p 00000000 00:00 0 7efced020000-7efcf0000000 ---p 00000000 00:00 0 7efcf1f1f000-7efd30000000 rw-p 00000000 00:00 0 7efd30000000-7efd30d6d000 rw-p 00000000 00:00 0 7efd30d6d000-7efd34000000 ---p 00000000 00:00 0 7efd37e44000-7efd51f22000 rw-p 00000000 00:00 0 7efd54000000-7efd56428000 rw-p 00000000 00:00 0 7efd56428000-7efd58000000 ---p 00000000 00:00 0 7efd59f22000-7efd80000000 rw-p 00000000 00:00 0 7efd80000000-7efd81732000 rw-p 00000000 00:00 0 7efd81732000-7efd84000000 ---p 00000000 00:00 0 7efd85f17000-7efd99f19000 rw-p 00000000 00:00 0 7efd99f19000-7efd99f1a000 ---p 00000000 00:00 0 7efd99f1a000-7efd9df1a000 rw-p 00000000 00:00 0 [stack:26273] 7efd9df1a000-7efd9df1b000 ---p 00000000 00:00 0 7efd9df1b000-7efda1f1b000 rw-p 00000000 00:00 0 [stack:26272] 7efda1f1b000-7efda1f1c000 ---p 00000000 00:00 0 7efda1f1c000-7efda5f1c000 rw-p 00000000 00:00 0 [stack:26271] 7efda5f1c000-7efda5f1d000 ---p 00000000 00:00 0 7efda5f1d000-7efda9f1d000 rw-p 00000000 00:00 0 [stack:26270] 7efda9f1d000-7efda9f1e000 ---p 00000000 00:00 0 7efda9f1e000-7efdadf1e000 rw-p 00000000 00:00 0 [stack:26269] 7efdadf1e000-7efdadf1f000 ---p 00000000 00:00 0 7efdadf1f000-7efdc209d000 rw-p 00000000 00:00 0 [stack:26268] 7efdc209d000-7efdc209e000 ---p 00000000 00:00 0 7efdc209e000-7efdc609e000 rw-p 00000000 00:00 0 [stack:26267] 7efdc609e000-7efdc609f000 ---p 00000000 00:00 0 7efdc609f000-7efdcfffe000 rw-p 00000000 00:00 0 [stack:26266] 7efdcfffe000-7efdcffff000 ---p 00000000 00:00 0 7efdcffff000-7efdd3fff000 rw-p 00000000 00:00 0 [stack:26265] 7efdd3fff000-7efdd4000000 ---p 00000000 00:00 0 7efdd4000000-7efdd8000000 rw-p 00000000 00:00 0 [stack:26264] 7efdd8000000-7efdd9246000 rw-p 00000000 00:00 0 7efdd9246000-7efddc000000 ---p 00000000 00:00 0 7efddfe6a000-7efddfe6b000 rw-p 00000000 00:00 0 7efddfe6b000-7efddfe6c000 ---p 00000000 00:00 0 7efddfe6c000-7efde3e6c000 rw-p 00000000 00:00 0 [stack:26263] 7efde3e6c000-7efde3e6d000 ---p 00000000 00:00 0 7efde3e6d000-7efe3b739000 rw-p 00000000 00:00 0 [stack:26262] 7fff8bda0000-7fff8bec2000 rw-p 00000000 00:00 0 [stack] 7fff8bff7000-7fff8bff9000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

fritzsedlazeck commented 7 years ago

Hi David, thanks for reporting this. Its a known bug that we encountered also from others and our own experience. Would you mind updating NGMLR to 2.6 ( current release) and give it another try? Thanks Fritz

fritzsedlazeck commented 7 years ago

Hi David, did you had a chance to test the newer version? If it works we can close this issue. Thanks Fritz