Command terminated by signal 9

[kreyszhang]

Error message I just started learning this software, and I don't quite understand what this error means. what signal 9 means

full bug report $more /home/ubuntu/data/result/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align01/nextDenovo.sh.e hostname

• hostname cd /home/ubuntu/data/result/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align01
• cd /home/ubuntu/data/result/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align01 time /home/ubuntu/software/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -t 8 -x ava-ont /home/ubuntu/data/result/01_rundir/01.raw_align/input.seed.003.2bit /home/ubuntu/data/result/01_rundir/01.raw_align/ input.part.013.2bit -o input.seed.003.2bit.0.ovl;
• time /home/ubuntu/software/NextDenovo/bin/minimap2-nd --step 1 --dual=yes -t 8 -x ava-ont /home/ubuntu/data/result/01_rundir/01.raw_align/input.seed.003.2bit /home/ubuntu/data/result/01_rundir/01.raw_alig n/input.part.013.2bit -o input.seed.003.2bit.0.ovl [M::mm_idx_gen::1.4241.00] collected minimizers [M::mm_idx_gen::1.6061.06] sorted minimizers [M::main::1.6061.06] loaded/built the index for 3136 target sequence(s) [M::mm_mapopt_update::1.6301.06] mid_occ = 170 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 3136 [M::mm_idx_stat::1.646*1.06] distinct minimizers: 1028225 (86.31% are singletons); average occurrences: 1.915; average spacing: 2.962 Command terminated by signal 9 7.65user 0.76system 0:07.63elapsed 110%CPU (0avgtext+0avgdata 1281924maxresident)k 11584inputs+0outputs (19major+331545minor)pagefaults 0swaps

Genome characteristics PCR product 700bp

Config file Please paste the complete content of the Config file (run.cfg) to here. [General] job_type = local # local, slurm, sge, pbs, lsf job_prefix = nextDenovo task = all # all, correct, assemble rewrite = yes # yes/no deltmp = yes parallel_jobs = 20 # number of tasks used to run in parallel input_type = raw # raw, corrected read_type = ont # clr, ont, hifi input_fofn = input.fofn workdir = 01_rundir

[correct_option] read_cutoff = 400bp genome_size = 0.7M # estimated genome size sort_options = -m 40g -t 10 minimap2_options_raw = -t 8 pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage. correction_options = -p 15

[assemble_option] minimap2_options_cns = -t 8 nextgraph_options = -a 1

see https://nextdenovo.readthedocs.io/en/latest/OPTION.html for a detailed introduction about all the parameters

Operating system No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.4 LTS Release: 18.04 Codename: bionic

GCC Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)

Python Python 3.8.5

[moold]

you don't have enough memory, try parallel_jobs = 1 and pa_correction=1

[moold]

I just realized your genome is only 700k, I'm not sure if nextdenovo is suitable for this.

[kreyszhang]

I'm so grateful, this worked. This is a PCR product, so it is very short. And I'm not very good at this work , I don't know if there is any other assembly software suitable for short genome assembly with third-generation sequencing. I know that short genomes are not suitable for third-generation sequencing, but the time of TGS is shorter than NGS, so I still want to try it .