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
I am running NGMLR with a polyploid using raw PacBio reads. It always crashes with the following output. I have tried to check the validity of fastq using tools like Fastqvalidator and also tried to check the read number where the software crashed but it all looks quite normal. I also tried running the same dataset on two different machines but nothing seems to help. I also tried compiling ngmlr rather than using pre-compiled binaries the error looks almost similar.
I am running NGMLR with a polyploid using raw PacBio reads. It always crashes with the following output. I have tried to check the validity of fastq using tools like Fastqvalidator and also tried to check the read number where the software crashed but it all looks quite normal. I also tried running the same dataset on two different machines but nothing seems to help. I also tried compiling ngmlr rather than using pre-compiled binaries the error looks almost similar.
/mnt/big_storage/ngmlr-0.2.7/ngmlr -t 50 -r /mnt/big_storage/sra/Brassica_napus_v4.1.fa -q output.fastq.gz -o Tapidor_pacbio_Brassica_napus_v41.sam ngmlr 0.2.7 (build: Jun 25 2018 10:17:59, start: 2019-08-14.07:27:23) Contact: philipp.rescheneder@univie.ac.at Opening for output (SAM): Tapidor_pacbio_Brassica_napus_v41.sam Reading encoded reference from /mnt/big_storage/sra/Brassica_napus_v4.1.fa-enc.2.ngm Reading 850 Mbp from disk took 11.61s Reading reference index from /mnt/big_storage/sra/Brassica_napus_v4.1.fa-ht-13-2.2.ngm Reading from disk took 27.28s Opening query file output.fastq.gz Mapping reads... Processed: 274433 (0.80), R/S: 113.10, RL: 11585, Time: 4.26 3.00 48.38, Align: 0.97, 612, 0.86 Processed: 2171548 (0.80), R/S: 107.94, RL: 11553, Time: 4.99 3.00 46.47, Align: 0.97, 605, 0.86 Debug: PositionNM reallocated. Debug: PositionNM reallocated. Debug: PositionNM reallocated. *** glibc detected *** ngmlr: double free or corruption (!prev): 0x00007f0c28e6b0a0 *** ======= Backtrace: ========= [0x4d35d4] [0x4d8367] [0x417ce1] [0x418338] [0x419faf] [0x41f8df] [0x41ff5b] [0x4215cc] [0x423c5c] [0x42911f] [0x435b14] [0x435b77] [0x4143d5] [0x41451b] [0x414f1d] [0x41ce8d] [0x41bdb9] [0x449736] [0x4ed849] ======= Memory map: ======== 00400000-00587000 r-xp 00000000 fd:10 29163522 /mnt/big_storage/ngmlr-0.2.7/ngmlr 00787000-0078f000 rw-p 00187000 fd:10 29163522 /mnt/big_storage/ngmlr-0.2.7/ngmlr 0078f000-007ab000 rw-p 00000000 00:00 0 02794000-09194000 rw-p 00000000 00:00 0 [heap] 7f09fbe82000-7f0a0c000000 rw-p 00000000 00:00 0 7f0a0c000000-7f0a0d771000 rw-p 00000000 00:00 0 7f0a0d771000-7f0a10000000 ---p 00000000 00:00 0 7f0a13b86000-7f0a44000000 rw-p 00000000 00:00 0 7f0a44000000-7f0a48000000 rw-p 00000000 00:00 0 7f0a4c000000-7f0a4fffc000 rw-p 00000000 00:00 0 7f0a4fffc000-7f0a50000000 ---p 00000000 00:00 0 7f0a50000000-7f0a53ffe000 rw-p 00000000 00:00 0 7f0a53ffe000-7f0a54000000 ---p 00000000 00:00 0 7f0a54000000-7f0a57ffd000 rw-p 00000000 00:00 0 7f0a57ffd000-7f0a58000000 ---p 00000000 00:00 0 7f0a58000000-7f0a5bfff000 rw-p 00000000 00:00 0 7f0a5bfff000-7f0a5c000000 ---p 00000000 00:00 0 7f0a5c000000-7f0a5fff9000 rw-p 00000000 00:00 0 7f0a5fff9000-7f0a60000000 ---p 00000000 00:00 0 7f0a60ad2000-7f0b7156a000 rw-p 00000000 00:00 0 7f0b78000000-7f0b7991f000 rw-p 00000000 00:00 0 7f0b7991f000-7f0b7c000000 ---p 00000000 00:00 0 7f0b7c000000-7f0b7d9ca000 rw-p 00000000 00:00 0 7f0b7d9ca000-7f0b80000000 ---p 00000000 00:00 0 7f0b816e8000-7f0c1dbf7000 rw-p 00000000 00:00 0 7f0c20000000-7f0c21688000 rw-p 00000000 00:00 0 7f0c21688000-7f0c24000000 ---p 00000000 00:00 0 7f0c28000000-7f0c2ac53000 rw-p 00000000 00:00 0 7f0c2ac53000-7f0c2c000000 ---p 00000000 00:00 0 7f0c2dd75000-7f0e672e0000 rw-p 00000000 00:00 0 7f0e68000000-7f0e697fb000 rw-p 00000000 00:00 0 7f0e697fb000-7f0e6c000000 ---p 00000000 00:00 0 7f0e70000000-7f0e7171d000 rw-p 00000000 00:00 0 7f0e7171d000-7f0e74000000 ---p 00000000 00:00 0 7f0e7745e000-7f10364e1000 rw-p 00000000 00:00 0 7f1040000000-7f10418e4000 rw-p 00000000 00:00 0 7f10418e4000-7f1044000000 ---p 00000000 00:00 0 7f104665f000-7f122f6fd000 rw-p 00000000 00:00 0 7f122f6fd000-7f122f6fe000 ---p 00000000 00:00 0 7f122f6fe000-7f122fefe000 rw-p 00000000 00:00 0 7f122fefe000-7f122feff000 ---p 00000000 00:00 0 7f122feff000-7f12306ff000 rw-p 00000000 00:00 0 7f12306ff000-7f1230700000 ---p 00000000 00:00 0 7f1230700000-7f1230f00000 rw-p 00000000 00:00 0 7f1230f00000-7f1230f01000 ---p 00000000 00:00 0 7f1230f01000-7f1231701000 rw-p 00000000 00:00 0 7f1231701000-7f1231702000 ---p 00000000 00:00 0 7f1231702000-7f1231f02000 rw-p 00000000 00:00 0 7f1231f02000-7f1231f03000 ---p 00000000 00:00 0 7f1231f03000-7f1232703000 rw-p 00000000 00:00 0 7f1232703000-7f1232704000 ---p 00000000 00:00 0 7f1232704000-7f1232f04000 rw-p 00000000 00:00 0 7f1232f04000-7f1232f05000 ---p 00000000 00:00 0 7f1232f05000-7f1233705000 rw-p 00000000 00:00 0 7f1233705000-7f1233706000 ---p 00000000 00:00 0 7f1233706000-7f1233f06000 rw-p 00000000 00:00 0 7f1233f06000-7f1233f07000 ---p 00000000 00:00 0 7f1233f07000-7f1234707000 rw-p 00000000 00:00 0 7f1234707000-7f1234708000 ---p 00000000 00:00 0 7f1234708000-7f1234f08000 rw-p 00000000 00:00 0 7f1234f08000-7f1234f09000 ---p 00000000 00:00 0 7f1234f09000-7f1235709000 rw-p 00000000 00:00 0 7f1235709000-7f123570a000 ---p 00000000 00:00 0 7f123570a000-7f1235f0a000 rw-p 00000000 00:00 0 7f1235f0a000-7f1235f0b000 ---p 00000000 00:00 0 7f1235f0b000-7f123670b000 rw-p 00000000 00:00 0 7f123670b000-7f123670c000 ---p 00000000 00:00 0 7f123670c000-7f1236f0c000 rw-p 00000000 00:00 0 7f1236f0c000-7f1236f0d000 ---p 00000000 00:00 0 7f1236f0d000-7f123770d000 rw-p 00000000 00:00 0 7f123770d000-7f123770e000 ---p 00000000 00:00 0 7f123770e000-7f1237f0e000 rw-p 00000000 00:00 0 7f1237f0e000-7f1237f0f000 ---p 00000000 00:00 0 7f1237f0f000-7f123870f000 rw-p 00000000 00:00 0 7f123870f000-7f1238710000 ---p 00000000 00:00 0 7f1238710000-7f1238f10000 rw-p 00000000 00:00 0 7f1238f10000-7f1238f11000 ---p 00000000 00:00 0 7f1238f11000-7f1239711000 rw-p 00000000 00:00 0 7f1239711000-7f1239712000 ---p 00000000 00:00 0 7f1239712000-7f1239f12000 rw-p 00000000 00:00 0 7f1239f12000-7f1239f13000 ---p 00000000 00:00 0 7f1239f13000-7f123a713000 rw-p 00000000 00:00 0 7f123a713000-7f123a714000 ---p 00000000 00:00 0 7f123a714000-7f123af14000 rw-p 00000000 00:00 0 7f123af14000-7f123af15000 ---p 00000000 00:00 0 7f123af15000-7f123b715000 rw-p 00000000 00:00 0 7f123b715000-7f123b716000 ---p 00000000 00:00 0 7f123b716000-7f123bf16000 rw-p 00000000 00:00 0 7f123bf16000-7f123bf17000 ---p 00000000 00:00 0 7f123bf17000-7f123c717000 rw-p 00000000 00:00 0 7f123c717000-7f123c718000 ---p 00000000 00:00 0 7f123c718000-7f1252ff5000 rw-p 00000000 00:00 0 7f1252ff5000-7f1252ff6000 ---p 00000000 00:00 0 7f1252ff6000-7f12537f6000 rw-p 00000000 00:00 0 7f12537f6000-7f12537f7000 ---p 00000000 00:00 0 7f12537f7000-7f1253ff7000 rw-p 00000000 00:00 0 7f1253ff7000-7f1253ff8000 ---p 00000000 00:00 0 7f1253ff8000-7f12547f8000 rw-p 00000000 00:00 0 7f12547f8000-7f12547f9000 ---p 00000000 00:00 0 7f12547f9000-7f1254ff9000 rw-p 00000000 00:00 0 7f1254ff9000-7f1254ffa000 ---p 00000000 00:00 0 7f1254ffa000-7f12557fa000 rw-p 00000000 00:00 0 7f12557fa000-7f12557fb000 ---p 00000000 00:00 0 7f12557fb000-7f1255ffb000 rw-p 00000000 00:00 0 7f1255ffb000-7f1255ffc000 ---p 00000000 00:00 0 7f1255ffc000-7f12567fc000 rw-p 00000000 00:00 0 7f12567fc000-7f12567fd000 ---p 00000000 00:00 0 7f12567fd000-7f1256ffd000 rw-p 00000000 00:00 0 7f1256ffd000-7f1256ffe000 ---p 00000000 00:00 0 7f1256ffe000-7f12577fe000 rw-p 00000000 00:00 0 7f12577fe000-7f12577ff000 ---p 00000000 00:00 0 7f12577ff000-7f125c000000 rw-p 00000000 00:00 0 7f125c000000-7f125fffc000 rw-p 00000000 00:00 0 7f125fffc000-7f1260000000 ---p 00000000 00:00 0 7f1260096000-7f126015a000 rw-p 00000000 00:00 0 7f12606e2000-7f126071d000 rw-p 00000000 00:00 0 7f126071d000-7f126071e000 ---p 00000000 00:00 0 7f126071e000-7f1260f1e000 rw-p 00000000 00:00 0 7f1260f1e000-7f1260f1f000 ---p 00000000 00:00 0 7f1260f1f000-7f126171f000 rw-p 00000000 00:00 0 7f126171f000-7f1261720000 ---p 00000000 00:00 0 7f1261720000-7f129c000000 rw-p 00000000 00:00 0 7f129c000000-7f129fffe000 rw-p 00000000 00:00 0 7f129fffe000-7f12a0000000 ---p 00000000 00:00 0 7f12a0043000-7f12a0142000 rw-p 00000000 00:00 0 7f12a017d000-7f12a01b8000 rw-p 00000000 00:00 0 7f12a03cb000-7f12a0406000 rw-p 00000000 00:00 0 7f12a0441000-7f12a0442000 ---p 00000000 00:00 0 7f12a0442000-7f12a0c42000 rw-p 00000000 00:00 0 7f12a0c7d000-7f12a0c7e000 ---p 00000000 00:00 0 7f12a0c7e000-7f12a147e000 rw-p 00000000 00:00 0 7f12a14b9000-7f12a14ba000 ---p 00000000 00:00 0 7f12a14ba000-7f12a1cba000 rw-p 00000000 00:00 0 7f12a1cf5000-7f12a1cf6000 ---p 00000000 00:00 0 7f12a1cf6000-7f12a24f6000 rw-p 00000000 00:00 0 7f12a2531000-7f12a2532000 ---p 00000000 00:00 0 7f12a2532000-7f12a2d32000 rw-p 00000000 00:00 0 7f12a2d6d000-7f12a2d6e000 ---p 00000000 00:00 0 7f12a2d6e000-7f12a3632000 rw-p 00000000 00:00 0 7f12a366d000-7f12a366e000 ---p 00000000 00:00 0 7f12a366e000-7f12a3e6e000 rw-p 00000000 00:00 0 7f12a3ea9000-7f12a3eaa000 ---p 00000000 00:00 0 7f12a3eaa000-7f12ba84b000 rw-p 00000000 00:00 0 7f12ba886000-7f12ba887000 ---p 00000000 00:00 0 7f12ba887000-7f12bb087000 rw-p 00000000 00:00 0 7f12bb0c2000-7f12bb0c3000 ---p 00000000 00:00 0 7f12bb0c3000-7f12bb8c3000 rw-p 00000000 00:00 0 7f12bb8fe000-7f13227fe000 rw-p 00000000 00:00 0 7ffc30d14000-7ffc30d35000 rw-p 00000000 00:00 0 [stack] 7ffc30d8d000-7ffc30d90000 r--p 00000000 00:00 0 [vvar] 7ffc30d90000-7ffc30d92000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)