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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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Core dump on Ubuntu 16.04 #20

Closed colindaven closed 7 years ago

colindaven commented 7 years ago

Hi,

I am getting a core dump on a bioconda compiled recent version 0.2.4. ngmlr 0.2.4 (build: May 18 2017 12:08:24, start: 2017-05-23.15:39:20)

Can't share the data because of data protection issues, sorry. These are certainly not long reads, about 3kbp N50. Aligning with 20 cores vs hg19.

7f9f3b800000-7f9f3c000000 rw-p 00000000 00:00 0 7f9f3c000000-7f9f3c9ae000 rw-p 00000000 00:00 0 7f9f3c9ae000-7f9f40000000 ---p 00000000 00:00 0 7f9f40094000-7f9f40095000 ---p 00000000 00:00 0 7f9f40095000-7f9f40895000 rw-p 00000000 00:00 0 7f9f40895000-7f9f40896000 ---p 00000000 00:00 0 7f9f40896000-7f9f41096000 rw-p 00000000 00:00 0 7f9f41096000-7f9f41097000 ---p 00000000 00:00 0 7f9f41097000-7f9f41897000 rw-p 00000000 00:00 0 7f9f41897000-7f9f41898000 ---p 00000000 00:00 0 7f9f41898000-7fa07c92e000 rw-p 00000000 00:00 0 7fa07c92e000-7fa07caed000 r-xp 00000000 08:02 5384958 /lib/x86_64-linux-gnu/libc-2.23.so 7fa07caed000-7fa07cced000 ---p 001bf000 08:02 5384958 /lib/x86_64-linux-gnu/libc-2.23.so 7fa07cced000-7fa07ccf1000 r--p 001bf000 08:02 5384958 /lib/x86_64-linux-gnu/libc-2.23.so 7fa07ccf1000-7fa07ccf3000 rw-p 001c3000 08:02 5384958 /lib/x86_64-linux-gnu/libc-2.23.so 7fa07ccf3000-7fa07ccf7000 rw-p 00000000 00:00 0 7fa07ccf7000-7fa07cd0d000 r-xp 00000000 00:2a 2450403566 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1 7fa07cd0d000-7fa07cf0c000 ---p 00016000 00:2a 2450403566 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1 7fa07cf0c000-7fa07cf0d000 rw-p 00015000 00:2a 2450403566 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1 7fa07cf0d000-7fa07cf0e000 rw-p 00074000 00:2a 2450403566 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1 7fa07cf0e000-7fa07d016000 r-xp 00000000 08:02 5384950 /lib/x86_64-linux-gnu/libm-2.23.so 7fa07d016000-7fa07d215000 ---p 00108000 08:02 5384950 /lib/x86_64-linux-gnu/libm-2.23.so 7fa07d215000-7fa07d216000 r--p 00107000 08:02 5384950 /lib/x86_64-linux-gnu/libm-2.23.so 7fa07d216000-7fa07d217000 rw-p 00108000 08:02 5384950 /lib/x86_64-linux-gnu/libm-2.23.so 7fa07d217000-7fa07d382000 r-xp 00000000 00:2a 2450392931 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21 7fa07d382000-7fa07d582000 ---p 0016b000 00:2a 2450392931 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21 7fa07d582000-7fa07d58c000 r--p 0016b000 00:2a 2450392931 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21 7fa07d58c000-7fa07d58e000 rw-p 00175000 00:2a 2450392931 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21 7fa07d58e000-7fa07d592000 rw-p 00000000 00:00 0 7fa07d592000-7fa07d5d3000 rw-p 00178000 00:2a 2450392931 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21 7fa07d5d3000-7fa07d5eb000 r-xp 00000000 08:02 5385490 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fa07d5eb000-7fa07d7ea000 ---p 00018000 08:02 5385490 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fa07d7ea000-7fa07d7eb000 r--p 00017000 08:02 5385490 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fa07d7eb000-7fa07d7ec000 rw-p 00018000 08:02 5385490 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fa07d7ec000-7fa07d7f0000 rw-p 00000000 00:00 0 7fa07d7f0000-7fa07d806000 r-xp 00000000 00:2a 2450422365 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8 7fa07d806000-7fa07da05000 ---p 00016000 00:2a 2450422365 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8 7fa07da05000-7fa07da06000 rw-p 00015000 00:2a 2450422365 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8 7fa07da06000-7fa07da2c000 r-xp 00000000 08:02 5384962 /lib/x86_64-linux-gnu/ld-2.23.so 7fa07dc09000-7fa07dc0e000 rw-p 00000000 00:00 0 7fa07dc28000-7fa07dc2b000 rw-p 00000000 00:00 0 7fa07dc2b000-7fa07dc2c000 r--p 00025000 08:02 5384962 /lib/x86_64-linux-gnu/ld-2.23.so 7fa07dc2c000-7fa07dc2d000 rw-p 00026000 08:02 5384962 /lib/x86_64-linux-gnu/ld-2.23.so 7fa07dc2d000-7fa07dc2e000 rw-p 00000000 00:00 0 7fff35142000-7fff35164000 rw-p 00000000 00:00 0 [stack] 7fff3517f000-7fff35181000 r--p 00000000 00:00 0 [vvar] 7fff35181000-7fff35183000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

[1]+ Aborted (core dumped) ngmlr -t 20 -r /lager2/rcug/seqres/HS/bwa/hg19.fa -q ../BRCA2_dup_allreads.fastq -o BRCA2_dup_allreads_ngmlr.sam -x ont

colindaven commented 7 years ago

This also happens when just rerunning the same command on one thread (just tested).

fritzsedlazeck commented 7 years ago

Could you send us the complete log for that run? Thanks Fritz

colindaven commented 7 years ago

Hi Fritz,

I don't have that log, but here is another with the same data. Albeit on a different machine, CentOS 5.5 with older kernel. 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux.

Package also installed with conda ngmlr --version ngmlr 0.2.4 (build: May 18 2017 12:08:24, start: 2017-05-31.03:50:35)

I will redo on the original Ubuntu 16.04 machine and post below

ngmlr -t 47 -r /lager2/rcug/seqres/HS/hg19.fa -q ../BRCA2_dup_allreads.fastq -o BRCA2_dup_allreads_ngmlr.sam -x ont 1> out1.log 2>out1err.log &

[rcug@localhost ngmlr]$ *** glibc detected *** ngmlr: free(): invalid next size (fast): 0x00007f5e3c20fa80 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3893475f4e]
/lib64/libc.so.6[0x3893478cf0]
ngmlr(_ZN5Align11clearBufferEv+0x2d)[0x43a45d]
ngmlr(_ZN15AlignmentBuffer16computeAlignmentEPK8IntervaliPKcmiiiPK10MappedReadbbb+0xc1d)[0x431b3d]
ngmlr(_ZN15AlignmentBuffer13alignIntervalEPK10MappedReadPK8IntervalPKcmbb+0x1ee)[0x43324e]
ngmlr(_ZN15AlignmentBuffer30alignSingleOrMultipleIntervalsEP10MappedReadPK8IntervalP13LocationScoreP5AlignRi+0x6e)[0x43692e]
ngmlr(_ZN15AlignmentBuffer18processLongReadLISEP9ReadGroup+0x21e2)[0x43a1d2]
ngmlr[0x447e91]
ngmlr(_ZN11ScoreBuffer7addReadEP10MappedReadi+0x58)[0x447f98]
ngmlr(_ZN2CS7RunReadEP10MappedReadPFvmymmPvEP11ScoreBufferP15AlignmentBuffer+0x26f)[0x42649f]
ngmlr(_ZN2CS8RunBatchEP11ScoreBufferP15AlignmentBuffer+0x4b)[0x42656b]
ngmlr(_ZN2CS5DoRunEv+0x80d)[0x424d1d]
ngmlr(_ZN7NGMTask3RunEv+0xd)[0x42d7bd]
ngmlr(_ZN4_NGM10ThreadFuncEPv+0x19)[0x42c529]
/lib64/libpthread.so.0[0x3893807aa1]
/lib64/libc.so.6(clone+0x6d)[0x38934e893d]
======= Memory map: ========
00400000-00462000 r-xp 00000000 08:03 11802771                           /home/rcug/tools/miniconda3/bin/ngmlr
00661000-00662000 rw-p 00061000 08:03 11802771                           /home/rcug/tools/miniconda3/bin/ngmlr
00662000-00663000 rw-p 00000000 00:00 0 
00869000-01361000 rw-p 00000000 00:00 0                                  [heap]
3892c00000-3892c20000 r-xp 00000000 08:03 7602589                        /lib64/ld-2.12.so
3892e1f000-3892e20000 r--p 0001f000 08:03 7602589                        /lib64/ld-2.12.so
3892e20000-3892e21000 rw-p 00020000 08:03 7602589                        /lib64/ld-2.12.so
3892e21000-3892e22000 rw-p 00000000 00:00 0 
3893400000-389358a000 r-xp 00000000 08:03 7602590                        /lib64/libc-2.12.so
389358a000-389378a000 ---p 0018a000 08:03 7602590                        /lib64/libc-2.12.so
389378a000-389378e000 r--p 0018a000 08:03 7602590                        /lib64/libc-2.12.so
389378e000-389378f000 rw-p 0018e000 08:03 7602590                        /lib64/libc-2.12.so
389378f000-3893794000 rw-p 00000000 00:00 0 
3893800000-3893817000 r-xp 00000000 08:03 7602597                        /lib64/libpthread-2.12.so
3893817000-3893a17000 ---p 00017000 08:03 7602597                        /lib64/libpthread-2.12.so
3893a17000-3893a18000 r--p 00017000 08:03 7602597                        /lib64/libpthread-2.12.so
3893a18000-3893a19000 rw-p 00018000 08:03 7602597                        /lib64/libpthread-2.12.so
3893a19000-3893a1d000 rw-p 00000000 00:00 0 
3894000000-3894083000 r-xp 00000000 08:03 7602603                        /lib64/libm-2.12.so
3894083000-3894282000 ---p 00083000 08:03 7602603                        /lib64/libm-2.12.so
3894282000-3894283000 r--p 00082000 08:03 7602603                        /lib64/libm-2.12.so
3894283000-3894284000 rw-p 00083000 08:03 7602603                        /lib64/libm-2.12.so
7f59e9316000-7f59f9494000 rw-p 00000000 00:00 0 
7f5a2990e000-7f5a39a8c000 rw-p 00000000 00:00 0 
7f5a49c0a000-7f5a7a084000 rw-p 00000000 00:00 0 
7f5a8a202000-7f5a9a380000 rw-p 00000000 00:00 0 
7f5aaa4fe000-7f5aca7fa000 rw-p 00000000 00:00 0 
7f5ada978000-7f5b2b0ee000 rw-p 00000000 00:00 0 
7f5b3b26c000-7f5b4b3ea000 rw-p 00000000 00:00 0 
7f5b5b568000-7f5b7b864000 rw-p 00000000 00:00 0 
7f5b8b9e2000-7f5bbbe5c000 rw-p 00000000 00:00 0 
7f5bbc2c6000-7f5bdc5c2000 rw-p 00000000 00:00 0 
7f5bec740000-7f5bfc8be000 rw-p 00000000 00:00 0 
7f5c0ca3c000-7f5c1cbba000 rw-p 00000000 00:00 0 
7f5c2cd38000-7f5c3ceb6000 rw-p 00000000 00:00 0 
7f5c4d034000-7f5c7d4ae000 rw-p 00000000 00:00 0 
7f5c8d62c000-7f5cad928000 rw-p 00000000 00:00 0 
7f5cbdaa6000-7f5d01f22000 rw-p 00000000 00:00 0 
7f5d120a0000-7f5d1c000000 rw-p 00000000 00:00 0 
7f5d1c000000-7f5d1c741000 rw-p 00000000 00:00 0 
7f5d1c741000-7f5d20000000 ---p 00000000 00:00 0 
7f5d21f21000-7f5d31f22000 rw-p 00000000 00:00 0 
7f5d420a0000-7f5d4c000000 rw-p 00000000 00:00 0 
7f5d4c000000-7f5d4d0b0000 rw-p 00000000 00:00 0 
7f5d4d0b0000-7f5d50000000 ---p 00000000 00:00 0 
7f5d51f21000-7f5d61f22000 rw-p 00000000 00:00 0 
7f5d720a0000-7f5d7c000000 rw-p 00000000 00:00 0 
7f5d7c000000-7f5d7c6a7000 rw-p 00000000 00:00 0 
7f5d7c6a7000-7f5d80000000 ---p 00000000 00:00 0 
7f5d81f21000-7f5d91f22000 rw-p 00000000 00:00 0 
7f5da20a0000-7f5dac000000 rw-p 00000000 00:00 0 
7f5dac000000-7f5dac72f000 rw-p 00000000 00:00 0 
7f5dac72f000-7f5db0000000 ---p 00000000 00:00 0 
7f5db1f21000-7f5dc1f22000 rw-p 00000000 00:00 0 
7f5dd20a0000-7f5ddc000000 rw-p 00000000 00:00 0 
7f5ddc000000-7f5ddc7a7000 rw-p 00000000 00:00 0 
7f5ddc7a7000-7f5de0000000 ---p 00000000 00:00 0 
7f5de1f21000-7f5df1f22000 rw-p 00000000 00:00 0 
7f5e020a0000-7f5e0c000000 rw-p 00000000 00:00 0 
7f5e0c000000-7f5e0c747000 rw-p 00000000 00:00 0 
7f5e0c747000-7f5e10000000 ---p 00000000 00:00 0 
7f5e11f21000-7f5e21f22000 rw-p 00000000 00:00 0 
7f5e320a0000-7f5e3c000000 rw-p 00000000 00:00 0 
7f5e3c000000-7f5e3c655000 rw-p 00000000 00:00 0 
7f5e3c655000-7f5e40000000 ---p 00000000 00:00 0 
7f5e43d7e000-7f5e53d7f000 rw-p 00000000 00:00 0 
7f5e63efd000-7f5e6de5d000 rw-p 00000000 00:00 0 
7f5e70000000-7f5e70739000 rw-p 00000000 00:00 0 
7f5e70739000-7f5e74000000 ---p 00000000 00:00 0 
7f5e75e5d000-7f5ea0000000 rw-p 00000000 00:00 0 
7f5ea0000000-7f5ea06b6000 rw-p 00000000 00:00 0 
7f5ea06b6000-7f5ea4000000 ---p 00000000 00:00 0 
7f5ea5d8f000-7f5eb5e54000 rw-p 00000000 00:00 0 
7f5ec60a0000-7f5ed0000000 rw-p 00000000 00:00 0 
7f5ed0000000-7f5ed08a1000 rw-p 00000000 00:00 0 
7f5ed08a1000-7f5ed4000000 ---p 00000000 00:00 0 
7f5ed5e5d000-7f5ee5f22000 rw-p 00000000 00:00 0 
7f5ef60a0000-7f5f00000000 rw-p 00000000 00:00 0 
7f5f00000000-7f5f00652000 rw-p 00000000 00:00 0 
7f5f00652000-7f5f04000000 ---p 00000000 00:00 0 
7f5f05b9c000-7f5f15b9d000 rw-p 00000000 00:00 0 
7f5f15e5e000-7f5f15f22000 rw-p 00000000 00:00 0 
7f5f260a0000-7f5f30000000 rw-p 00000000 00:00 0 
7f5f30000000-7f5f30663000 rw-p 00000000 00:00 0 
7f5f30663000-7f5f34000000 ---p 00000000 00:00 0 
7f5f35e5d000-7f5f45f22000 rw-p 00000000 00:00 0 
7f5f560a0000-7f5f60000000 rw-p 00000000 00:00 0 
7f5f60000000-7f5f60662000 rw-p 00000000 00:00 0 
7f5f60662000-7f5f64000000 ---p 00000000 00:00 0 
7f5f65e5d000-7f5f90000000 rw-p 00000000 00:00 0 
7f5f90000000-7f5f9061e000 rw-p 00000000 00:00 0 
7f5f9061e000-7f5f94000000 ---p 00000000 00:00 0 
7f5f95d98000-7f5fa5d99000 rw-p 00000000 00:00 0 
7f5fa5e5e000-7f5fc0000000 rw-p 00000000 00:00 0 
7f5fc0000000-7f5fc0644000 rw-p 00000000 00:00 0 
7f5fc0644000-7f5fc4000000 ---p 00000000 00:00 0 
7f5fc5e5d000-7f5fd5f22000 rw-p 00000000 00:00 0 
7f5fe60a0000-7f5ff0000000 rw-p 00000000 00:00 0 
7f5ff0000000-7f5ff0627000 rw-p 00000000 00:00 0 
7f5ff0627000-7f5ff4000000 ---p 00000000 00:00 0 
7f5ff5dd6000-7f6005dd7000 rw-p 00000000 00:00 0 
7f6005e5e000-7f6005f22000 rw-p 00000000 00:00 0 
7f60160a0000-7f6020000000 rw-p 00000000 00:00 0 
7f6020000000-7f60205ec000 rw-p 00000000 00:00 0 
7f60205ec000-7f6024000000 ---p 00000000 00:00 0 
7f6025f21000-7f6050000000 rw-p 00000000 00:00 0 
7f6050000000-7f60505df000 rw-p 00000000 00:00 0 
7f60505df000-7f6054000000 ---p 00000000 00:00 0 
7f6057d7f000-7f6067e44000 rw-p 00000000 00:00 0 
7f6077fc2000-7f6081f22000 rw-p 00000000 00:00 0 
7f6084000000-7f6084648000 rw-p 00000000 00:00 0 
7f6084648000-7f6088000000 ---p 00000000 00:00 0 
7f6089f22000-7f6099f23000 rw-p 00000000 00:00 0 
7f60aa0a1000-7f60b0000000 rw-p 00000000 00:00 0 
7f60b0000000-7f60b06c0000 rw-p 00000000 00:00 0 
7f60b06c0000-7f60b4000000 ---p 00000000 00:00 0 
7f60b5e5c000-7f60c9f22000 rw-p 00000000 00:00 0 
7f60da0a0000-7f60e4000000 rw-p 00000000 00:00 0 
7f60e4000000-7f60e4637000 rw-p 00000000 00:00 0 
7f60e4637000-7f60e8000000 ---p 00000000 00:00 0 
7f60e9dca000-7f60f9dcb000 rw-p 00000000 00:00 0 
7f60f9e5e000-7f60f9f22000 rw-p 00000000 00:00 0 
7f610a0a0000-7f6114000000 rw-p 00000000 00:00 0 
7f6114000000-7f611468d000 rw-p 00000000 00:00 0 
7f611468d000-7f6118000000 ---p 00000000 00:00 0 
7f6119e5d000-7f6129f22000 rw-p 00000000 00:00 0 
7f613a0a0000-7f6144000000 rw-p 00000000 00:00 0 
7f6144000000-7f6144691000 rw-p 00000000 00:00 0 
7f6144691000-7f6148000000 ---p 00000000 00:00 0 
7f6149e5d000-7f6159f22000 rw-p 00000000 00:00 0 
7f616a0a0000-7f6174000000 rw-p 00000000 00:00 0 
7f6174000000-7f617461d000 rw-p 00000000 00:00 0 
7f617461d000-7f6178000000 ---p 00000000 00:00 0 
7f6179e5d000-7f6189f22000 rw-p 00000000 00:00 0 
7f619a0a0000-7f61a4000000 rw-p 00000000 00:00 0 
7f61a4000000-7f61a4705000 rw-p 00000000 00:00 0 
7f61a4705000-7f61a8000000 ---p 00000000 00:00 0 
7f61a9e5d000-7f61b9f22000 rw-p 00000000 00:00 0 
7f61ca0a0000-7f61d4000000 rw-p 00000000 00:00 0 
7f61d4000000-7f61d466c000 rw-p 00000000 00:00 0 
7f61d466c000-7f61d8000000 ---p 00000000 00:00 0 
7f61d9e5d000-7f61e9f22000 rw-p 00000000 00:00 0 
7f61fa0a0000-7f6204000000 rw-p 00000000 00:00 0 
7f6204000000-7f620468e000 rw-p 00000000 00:00 0 
7f620468e000-7f6208000000 ---p 00000000 00:00 0 
7f6209e5d000-7f6219f22000 rw-p 00000000 00:00 0 
7f622a0a0000-7f6234000000 rw-p 00000000 00:00 0 
7f6234000000-7f62345e3000 rw-p 00000000 00:00 0 
7f62345e3000-7f6238000000 ---p 00000000 00:00 0 
7f6239e5d000-7f6264000000 rw-p 00000000 00:00 0 
7f6264000000-7f6264900000 rw-p 00000000 00:00 0 
7f6264900000-7f6268000000 ---p 00000000 00:00 0 
7f6269f22000-7f6279f23000 rw-p 00000000 00:00 0 
7f628a0a1000-7f6290000000 rw-p 00000000 00:00 0 
7f6290000000-7f62906bc000 rw-p 00000000 00:00 0 
7f62906bc000-7f6294000000 ---p 00000000 00:00 0 
7f6295e5c000-7f62a9f22000 rw-p 00000000 00:00 0 
7f62ba0a0000-7f62c4000000 rw-p 00000000 00:00 0 
7f62c4000000-7f62c46ad000 rw-p 00000000 00:00 0 
7f62c46ad000-7f62c8000000 ---p 00000000 00:00 0 
7f62c9e5d000-7f62d9f22000 rw-p 00000000 00:00 0 
7f62ea0a0000-7f62f4000000 rw-p 00000000 00:00 0 
7f62f4000000-7f62f4679000 rw-p 00000000 00:00 0 
7f62f4679000-7f62f8000000 ---p 00000000 00:00 0 
7f62f9e5d000-7f6309f22000 rw-p 00000000 00:00 0 
7f631a0a0000-7f6324000000 rw-p 00000000 00:00 0 
7f6324000000-7f6324660000 rw-p 00000000 00:00 0 
7f6324660000-7f6328000000 ---p 00000000 00:00 0 
7f6329e5d000-7f6339f22000 rw-p 00000000 00:00 0 
7f634a0a0000-7f6354000000 rw-p 00000000 00:00 0 
7f6354000000-7f635468f000 rw-p 00000000 00:00 0 
7f635468f000-7f6358000000 ---p 00000000 00:00 0 
7f6359e5d000-7f6369f22000 rw-p 00000000 00:00 0 
7f637a0a0000-7f6384000000 rw-p 00000000 00:00 0 
7f6384000000-7f6384647000 rw-p 00000000 00:00 0 
7f6384647000-7f6388000000 ---p 00000000 00:00 0 
7f6389e5d000-7f63b4000000 rw-p 00000000 00:00 0 
7f63b4000000-7f63b464a000 rw-p 00000000 00:00 0 
7f63b464a000-7f63b8000000 ---p 00000000 00:00 0 
7f63b9f22000-7f63c9f23000 rw-p 00000000 00:00 0 
7f63da0a1000-7f63e0000000 rw-p 00000000 00:00 0 
7f63e0000000-7f63e07e0000 rw-p 00000000 00:00 0 
7f63e07e0000-7f63e4000000 ---p 00000000 00:00 0 
7f63e5e5c000-7f6414000000 rw-p 00000000 00:00 0 
7f6414000000-7f6414679000 rw-p 00000000 00:00 0 
7f6414679000-7f6418000000 ---p 00000000 00:00 0 
7f6419f22000-7f6440000000 rw-p 00000000 00:00 0 
7f6440000000-7f6440697000 rw-p 00000000 00:00 0 
7f6440697000-7f6444000000 ---p 00000000 00:00 0 
7f6445e5c000-7f6474000000 rw-p 00000000 00:00 0 
7f6474000000-7f647467e000 rw-p 00000000 00:00 0 
7f647467e000-7f6478000000 ---p 00000000 00:00 0 
7f6479f21000-7f6489f22000 rw-p 00000000 00:00 0 
7f6494000000-7f6494021000 rw-p 00000000 00:00 0 
7f6494021000-7f6498000000 ---p 00000000 00:00 0 
7f649a0a0000-7f64a4000000 rw-p 00000000 00:00 0 
7f64a4000000-7f64a467a000 rw-p 00000000 00:00 0 
7f64a467a000-7f64a8000000 ---p 00000000 00:00 0 
7f64ab659000-7f64bb65a000 rw-p 00000000 00:00 0 
7f64bb65a000-7f64bb65b000 ---p 00000000 00:00 0 
7f64bb65b000-7f64bc05b000 rw-p 00000000 00:00 0 
7f64bc05b000-7f64bc05c000 ---p 00000000 00:00 0 
7f64bc05c000-7f64bca5c000 rw-p 00000000 00:00 0 
7f64bca5c000-7f64bca5d000 ---p 00000000 00:00 0 
7f64bca5d000-7f64bd45d000 rw-p 00000000 00:00 0 
7f64bd45d000-7f64bd45e000 ---p 00000000 00:00 0 
7f64bd45e000-7f64d8000000 rw-p 00000000 00:00 0 
7f64d8000000-7f64d86ba000 rw-p 00000000 00:00 0 
7f64d86ba000-7f64dc000000 ---p 00000000 00:00 0 
7f64dd856000-7f64dd857000 ---p 00000000 00:00 0 
7f64dd857000-7f64ee258000 rw-p 00000000 00:00 0 
7f64ee258000-7f64ee259000 ---p 00000000 00:00 0 
7f64ee259000-7f64eec59000 rw-p 00000000 00:00 0 
7f64eec59000-7f64eec5a000 ---p 00000000 00:00 0 
7f64eec5a000-7f64ef65a000 rw-p 00000000 00:00 0 
7f64ef65a000-7f64ef65b000 ---p 00000000 00:00 0 
7f64ef65b000-7f64f005b000 rw-p 00000000 00:00 0 
7f64f005b000-7f64f005c000 ---p 00000000 00:00 0 
7f64f005c000-7f64f0a5c000 rw-p 00000000 00:00 0 
7f64f0a5c000-7f64f0a5d000 ---p 00000000 00:00 0 
7f64f0a5d000-7f64f1521000 rw-p 00000000 00:00 0 
7f64f1521000-7f64f1522000 ---p 00000000 00:00 0 
7f64f1522000-7f650c000000 rw-p 00000000 00:00 0 
7f650c000000-7f650c609000 rw-p 00000000 00:00 0 
7f650c609000-7f6510000000 ---p 00000000 00:00 0 
7f6510454000-7f6510455000 ---p 00000000 00:00 0 
7f6510455000-7f6510e55000 rw-p 00000000 00:00 0 
7f6510e55000-7f6510e56000 ---p 00000000 00:00 0 
7f6510e56000-7f6521857000 rw-p 00000000 00:00 0 
7f6521857000-7f6521858000 ---p 00000000 00:00 0 
7f6521858000-7f6522258000 rw-p 00000000 00:00 0 
7f6522258000-7f6522259000 ---p 00000000 00:00 0 
7f6522259000-7f6522c59000 rw-p 00000000 00:00 0 
7f6522c59000-7f6522c5a000 ---p 00000000 00:00 0 
7f6522c5a000-7f652365a000 rw-p 00000000 00:00 0 
7f652365a000-7f652365b000 ---p 00000000 00:00 0 
7f652365b000-7f652405b000 rw-p 00000000 00:00 0 
7f652405b000-7f652405c000 ---p 00000000 00:00 0 
7f652405c000-7f6524a5c000 rw-p 00000000 00:00 0 
7f6524a5c000-7f6524a5d000 ---p 00000000 00:00 0 
7f6524a5d000-7f652545d000 rw-p 00000000 00:00 0 
7f652545d000-7f652545e000 ---p 00000000 00:00 0 
7f652545e000-7f6540000000 rw-p 00000000 00:00 0 
7f6540000000-7f6540667000 rw-p 00000000 00:00 0 
7f6540667000-7f6544000000 ---p 00000000 00:00 0 
7f6544454000-7f6544455000 ---p 00000000 00:00 0 
7f6544455000-7f6544e55000 rw-p 00000000 00:00 0 
7f6544e55000-7f6544e56000 ---p 00000000 00:00 0 
7f6544e56000-7f6555857000 rw-p 00000000 00:00 0 
7f6555857000-7f6555858000 ---p 00000000 00:00 0 
7f6555858000-7f6556258000 rw-p 00000000 00:00 0 
7f6556258000-7f6556259000 ---p 00000000 00:00 0 
7f6556259000-7f6556c59000 rw-p 00000000 00:00 0 
7f6556c59000-7f6556c5a000 ---p 00000000 00:00 0 
7f6556c5a000-7f655765a000 rw-p 00000000 00:00 0 
7f655765a000-7f655765b000 ---p 00000000 00:00 0 
7f655765b000-7f655805b000 rw-p 00000000 00:00 0 
7f655805b000-7f655805c000 ---p 00000000 00:00 0 
7f655805c000-7f6558a5c000 rw-p 00000000 00:00 0 
7f6558a5c000-7f6558a5d000 ---p 00000000 00:00 0 
7f6558a5d000-7f655945d000 rw-p 00000000 00:00 0 
7f655945d000-7f655945e000 ---p 00000000 00:00 0 
7f655945e000-7f6574000000 rw-p 00000000 00:00 0 
7f6574000000-7f6574684000 rw-p 00000000 00:00 0 
7f6574684000-7f6578000000 ---p 00000000 00:00 0 
7f6578e55000-7f6578e56000 ---p 00000000 00:00 0 
7f6578e56000-7f6579856000 rw-p 00000000 00:00 0 
7f6579856000-7f6579857000 ---p 00000000 00:00 0 
7f6579857000-7f658a258000 rw-p 00000000 00:00 0 
7f658a258000-7f658a259000 ---p 00000000 00:00 0 
7f658a259000-7f658ac59000 rw-p 00000000 00:00 0 
7f658ac59000-7f658ac5a000 ---p 00000000 00:00 0 
7f658ac5a000-7f658b65a000 rw-p 00000000 00:00 0 
7f658b65a000-7f658b65b000 ---p 00000000 00:00 0 
7f658b65b000-7f658c05b000 rw-p 00000000 00:00 0 
7f658c05b000-7f658c05c000 ---p 00000000 00:00 0 
7f658c05c000-7f658ca5c000 rw-p 00000000 00:00 0 
7f658ca5c000-7f658ca5d000 ---p 00000000 00:00 0 
7f658ca5d000-7f658d45d000 rw-p 00000000 00:00 0 
7f658d45d000-7f658d45e000 ---p 00000000 00:00 0 
7f658d45e000-7f65a8000000 rw-p 00000000 00:00 0 
7f65a8000000-7f65a891f000 rw-p 00000000 00:00 0 
7f65a891f000-7f65ac000000 ---p 00000000 00:00 0 
7f65ac820000-7f65ac821000 ---p 00000000 00:00 0 
7f65ac821000-7f65ad221000 rw-p 00000000 00:00 0 
7f65ad221000-7f65ad222000 ---p 00000000 00:00 0 
7f65ad222000-7f65bdc23000 rw-p 00000000 00:00 0 
7f65bdc23000-7f65bdc24000 ---p 00000000 00:00 0 
7f65bdc24000-7f66ac91f000 rw-p 00000000 00:00 0 
7f66adb9d000-7f66adc61000 rw-p 00000000 00:00 0 
7f66add91000-7f66b4000000 rw-p 00000000 00:00 0 
7f66b4000000-7f66b486f000 rw-p 00000000 00:00 0 
7f66b486f000-7f66b8000000 ---p 00000000 00:00 0 
7f66b8009000-7f66b8255000 rw-p 00000000 00:00 0 
7f66b8255000-7f66b8256000 ---p 00000000 00:00 0 
7f66b8256000-7f66b8c56000 rw-p 00000000 00:00 0 
7f66b8c56000-7f66b8c57000 ---p 00000000 00:00 0 
7f66b8c57000-7f66b9657000 rw-p 00000000 00:00 0 
7f66b9657000-7f66b9658000 ---p 00000000 00:00 0 
7f66b9658000-7f66ba058000 rw-p 00000000 00:00 0 
7f66ba058000-7f66ba059000 ---p 00000000 00:00 0 
7f66ba059000-7f66bab1d000 rw-p 00000000 00:00 0 
7f66bab1d000-7f66bab1e000 ---p 00000000 00:00 0 
7f66bab1e000-7f66bb51e000 rw-p 00000000 00:00 0 
7f66bb51e000-7f66bb51f000 ---p 00000000 00:00 0 
7f66bb51f000-7f66bbf1f000 rw-p 00000000 00:00 0 
7f66bbf1f000-7f66bbf20000 ---p 00000000 00:00 0 
7f66bbf20000-7f671913c000 rw-p 00000000 00:00 0 
7f671913c000-7f6719152000 r-xp 00000000 08:03 13634723                   /home/rcug/tools/miniconda3/lib/libgcc_s.so.1
7f6719152000-7f6719351000 ---p 00016000 08:03 13634723                   /home/rcug/tools/miniconda3/lib/libgcc_s.so.1
7f6719351000-7f6719352000 rw-p 00015000 08:03 13634723                   /home/rcug/tools/miniconda3/lib/libgcc_s.so.1
7f6719352000-7f6719353000 rw-p 00000000 00:00 0 
7f6719353000-7f671944a000 r-xp 00000000 08:03 13634772                   /home/rcug/tools/miniconda3/lib/libstdc++.so.6.0.19
7f671944a000-7f671964a000 ---p 000f7000 08:03 13634772                   /home/rcug/tools/miniconda3/lib/libstdc++.so.6.0.19
7f671964a000-7f6719651000 r--p 000f7000 08:03 13634772                   /home/rcug/tools/miniconda3/lib/libstdc++.so.6.0.19
7f6719651000-7f6719654000 rw-p 000fe000 08:03 13634772                   /home/rcug/tools/miniconda3/lib/libstdc++.so.6.0.19
7f6719654000-7f671966a000 rw-p 00000000 00:00 0 
7f6719672000-7f6719673000 rw-p 00000000 00:00 0 
7f6719673000-7f6719689000 r-xp 00000000 08:03 11800000                   /home/rcug/tools/miniconda3/lib/libz.so.1.2.8
7f6719689000-7f6719888000 ---p 00016000 08:03 11800000                   /home/rcug/tools/miniconda3/lib/libz.so.1.2.8
7f6719888000-7f6719889000 rw-p 00015000 08:03 11800000                   /home/rcug/tools/miniconda3/lib/libz.so.1.2.8
7f6719889000-7f671988a000 rw-p 00000000 00:00 0 
7ffda89b9000-7ffda89ce000 rw-p 00000000 00:00 0                          [stack]
7ffda89cf000-7ffda89d0000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

[1]+  Aborted                 (core dumped) ngmlr -t 47 -r /lager2/rcug/seqres/HS/hg19.fa -q ../BRCA2_dup_allreads.fastq -o BRCA2_dup_allreads_ngmlr.sam -x ont > out1.log 2> out1err.log
fritzsedlazeck commented 7 years ago

Thanks for posting that. could you also show me the last few lines from out1.log ? Thanks Fritz

colindaven commented 7 years ago

On the ubuntu 16.04 machine, the following error occurs. The stack trace is abruptly shortened, but one error message is

ESC[AESC[2KProcessed: 586103 (0.74), R/S: 102.44, RL: 7641, Time: 14.33 3.03 62.22, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 586346 (0.74), R/S: 102.44, RL: 7641, Time: 14.15 3.01 60.60, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 586562 (0.74), R/S: 102.45, RL: 7640, Time: 14.37 3.27 60.64, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 586742 (0.74), R/S: 102.44, RL: 7640, Time: 14.87 3.55 61.54, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 586914 (0.74), R/S: 102.44, RL: 7641, Time: 14.28 3.02 61.26, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 587067 (0.74), R/S: 102.43, RL: 7641, Time: 14.85 3.54 61.35, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 587243 (0.74), R/S: 102.42, RL: 7642, Time: 14.63 3.63 61.15, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 587435 (0.74), R/S: 102.42, RL: 7641, Time: 14.41 3.15 61.41, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 587667 (0.74), R/S: 102.42, RL: 7641, Time: 14.61 3.11 63.36, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 587893 (0.74), R/S: 102.43, RL: 7642, Time: 14.49 3.16 62.41, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 588113 (0.74), R/S: 102.42, RL: 7642, Time: 14.22 3.22 60.09, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 588326 (0.74), R/S: 102.43, RL: 7642, Time: 14.32 3.32 61.38, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 588533 (0.74), R/S: 102.43, RL: 7642, Time: 13.98 3.13 59.76, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 588729 (0.74), R/S: 102.42, RL: 7642, Time: 14.49 3.55 61.66, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 588958 (0.74), R/S: 102.43, RL: 7641, Time: 14.68 3.03 63.09, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 589142 (0.74), R/S: 102.42, RL: 7642, Time: 14.95 3.58 61.52, Align: 0.98, 440, 0.95
ESC[AESC[2KProcessed: 589355 (0.74), R/S: 102.43, RL: 7641, Time: 14.28 3.25 60.14, Align: 0.98, 440, 0.95
CIGAR/MD buffer not long enough. Please report this!
ESC[AESC[2KWarning: could not compute alignment for read a2e1a8f7-3362-486a-b285-ec93246af59e
7fac12272000-7fac12273000 ---p 00000000 00:00 0
7fac12273000-7fac12a73000 rw-p 00000000 00:00 0
7fac12a73000-7fac12a74000 ---p 00000000 00:00 0
7fac12a74000-7fac13274000 rw-p 00000000 00:00 0
7fac13274000-7fac13275000 ---p 00000000 00:00 0
7fac13275000-7fac13a75000 rw-p 00000000 00:00 0
7fac13a75000-7fac13a76000 ---p 00000000 00:00 0
7fac13a76000-7fac14276000 rw-p 00000000 00:00 0
7fac14276000-7fac14277000 ---p 00000000 00:00 0
7fac14277000-7fad4f30d000 rw-p 00000000 00:00 0
7fad4f30d000-7fad4f4cc000 r-xp 00000000 08:02 5384958                    /lib/x86_64-linux-gnu/libc-2.23.so
7fad4f4cc000-7fad4f6cc000 ---p 001bf000 08:02 5384958                    /lib/x86_64-linux-gnu/libc-2.23.so
7fad4f6cc000-7fad4f6d0000 r--p 001bf000 08:02 5384958                    /lib/x86_64-linux-gnu/libc-2.23.so
7fad4f6d0000-7fad4f6d2000 rw-p 001c3000 08:02 5384958                    /lib/x86_64-linux-gnu/libc-2.23.so
7fad4f6d2000-7fad4f6d6000 rw-p 00000000 00:00 0
7fad4f6d6000-7fad4f6ec000 r-xp 00000000 00:2a 2450403566                 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1
7fad4f6ec000-7fad4f8eb000 ---p 00016000 00:2a 2450403566                 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1
7fad4f8eb000-7fad4f8ec000 rw-p 00015000 00:2a 2450403566                 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1
7fad4f8ec000-7fad4f8ed000 rw-p 00074000 00:2a 2450403566                 /mnt/ngsnfs/tools/miniconda2/lib/libgcc_s.so.1
7fad4f8ed000-7fad4f9f5000 r-xp 00000000 08:02 5384950                    /lib/x86_64-linux-gnu/libm-2.23.so
7fad4f9f5000-7fad4fbf4000 ---p 00108000 08:02 5384950                    /lib/x86_64-linux-gnu/libm-2.23.so
7fad4fbf4000-7fad4fbf5000 r--p 00107000 08:02 5384950                    /lib/x86_64-linux-gnu/libm-2.23.so
7fad4fbf5000-7fad4fbf6000 rw-p 00108000 08:02 5384950                    /lib/x86_64-linux-gnu/libm-2.23.so
7fad4fbf6000-7fad4fd61000 r-xp 00000000 00:2a 2450392931                 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21
7fad4fd61000-7fad4ff61000 ---p 0016b000 00:2a 2450392931                 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21
7fad4ff61000-7fad4ff6b000 r--p 0016b000 00:2a 2450392931                 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21
7fad4ff6b000-7fad4ff6d000 rw-p 00175000 00:2a 2450392931                 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21
7fad4ff6d000-7fad4ff71000 rw-p 00000000 00:00 0
7fad4ff71000-7fad4ffb2000 rw-p 00178000 00:2a 2450392931                 /mnt/ngsnfs/tools/miniconda2/lib/libstdc++.so.6.0.21
7fad4ffb2000-7fad4ffca000 r-xp 00000000 08:02 5385490                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fad4ffca000-7fad501c9000 ---p 00018000 08:02 5385490                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fad501c9000-7fad501ca000 r--p 00017000 08:02 5385490                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fad501ca000-7fad501cb000 rw-p 00018000 08:02 5385490                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7fad501cb000-7fad501cf000 rw-p 00000000 00:00 0
7fad501cf000-7fad501e5000 r-xp 00000000 00:2a 2450422365                 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8
7fad501e5000-7fad503e4000 ---p 00016000 00:2a 2450422365                 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8
7fad503e4000-7fad503e5000 rw-p 00015000 00:2a 2450422365                 /mnt/ngsnfs/tools/miniconda2/lib/libz.so.1.2.8
7fad503e5000-7fad5040b000 r-xp 00000000 08:02 5384962                    /lib/x86_64-linux-gnu/ld-2.23.so
7fad505e8000-7fad505ed000 rw-p 00000000 00:00 0
7fad50607000-7fad5060a000 rw-p 00000000 00:00 0
7fad5060a000-7fad5060b000 r--p 00025000 08:02 5384962                    /lib/x86_64-linux-gnu/ld-2.23.so
7fad5060b000-7fad5060c000 rw-p 00026000 08:02 5384962                    /lib/x86_64-linux-gnu/ld-2.23.so
7fad5060c000-7fad5060d000 rw-p 00000000 00:00 0
7fff1fa93000-7fff1fab5000 rw-p 00000000 00:00 0                          [stack]
7fff1fbd9000-7fff1fbdb000 r--p 00000000 00:00 0                          [vvar]
7fff1fbdb000-7fff1fbdd000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

[1]+  Aborted                 (core dumped) ngmlr -t 18 -r /lager2/rcug/seqres/HS/bwa/hg19.fa -q ../BRCA2_dup_allreads.fastq -o BRCA2_dup_allreads_ngmlr.sam -x ont > out1.log 2> out1err.log
fritzsedlazeck commented 7 years ago

Hi that was the line that I was looking for: "CIGAR/MD buffer not long enough. Please report this!" We are testing a fix for that right now and Philipp will release it today or tomorrow if everything checks out. Thanks Fritz

philres commented 7 years ago

Hi,

sorry for the delay. We have implemented a potential fix for this problem. Would be great if you could try this ( ngmlr-0.2.5-dev-beta-linux-x86_64.tar.gz ) version of ngmlr on your data. If you prefer you can als compile it yourself. I pushed the changes to the master branch.

Thanks, Philipp

colindaven commented 7 years ago

Hi Philipp,

great, thanks. This fix resolved the issue on ont data. I did not recompile, but used your binary version.

Best wishes, Colin

philres commented 7 years ago

Great! Thanks for letting me know!

2017-06-20 10:55 GMT+02:00 Colin Davenport notifications@github.com:

Closed #20 https://github.com/philres/ngmlr/issues/20.

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