Closed Ural-Yunusbaev closed 2 years ago
Hi, The current version has bug that can not parse fastq file correctly for HiFi or corrected data, so you can transform the fastq file to fasta file.
Thanks!
Hi, I've encountered similar issue. nextDenovo worked with raw Nanopore reads, but when changing the input file into the corrected reads I got a similar error message. I've converted the fastq file to fasta file, but it still not worked.
Here is the error message:
File "/usr/local/bin/nextDenovo", line 856, in
It seems the genome_size you set is not correct, so could you paste your config file to here?
Hi, You are right! I accidentally set my genome_size to auto, and it's fixed after changing to the estimated genome size. Thanks for your help!
Best, Tzu-Haw
Hi @Ural-Yunusbaev,
I'm still trying to figure out how to run NextDenovo in a HPC environment using SLURM.
Would you be able to share your NextDenovo2.4_slurm.sh
and run.cfg
with me?
Describe the bug I run on nextDenovo in SLURM in 1 node using 60 cores & 70G RAM sbatch --nodes=1 --ntasks=1 --cpus-per-task=60 --mem=70G ./_NextDenovo2.4_slurm.sh
When I Run nextDenovo using test.ecoli.HiFi.fastq with read_type: hifi it reports: File ".../nextDenovo", line 856, in main(args) ... IndexError: list index out of range
Meantime when I run other types of reads of the same organism with
read_type: clr OR ont
it goes smoothly
I tried bac, insect, plant genomes with HiFi reads and had the same error. Meantime when I run the same organisms with CLR or ONT reads it goes smoothly.
Error message log message
Genome characteristics
ecoli 4.8m
Input data
ecoli 4.8m from https://sra-pub-src-1.s3.amazonaws.com/SRR10971019/m54316_180808_005743.fastq.1
Config file [General] job_type = local # local, slurm, sge, pbs, lsf job_prefix = nextDenovo task = assemble # all, correct, assemble rewrite = yes # yes/no deltmp = yes parallel_jobs = 2 # number of tasks used to run in parallel input_type = raw # raw, corrected read_type = hifi # clr, ont, hifi input_fofn = input.fofn workdir = 01_rundir
[correct_option] read_cutoff = 1k genome_size = 4.8m # estimated genome size
[assemble_option] minimap2_options_cns = -t 60 nextgraph_options = -a 1 # -q, min short branch len for output, 0=disable, set 5-16 to adjust the assembly size [0] .
Operating system Which operating system and version are you using? You can use the command
lsb_release -a
to get it. lsb_release -a bash: lsb_release: command not found...GCC What version of GCC are you using? You can use the command
gcc -v
to get it. gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)Python What version of Python are you using? You can use the command
python --version
to get it. python3 --version Python 3.6.8 head -1 /homes/ural/soft/NextDenovo2.4/NextDenovo/nextDenovo!/usr/bin/env python3
NextDenovo What version of NextDenovo are you using? You can use the command
nextDenovo -v
to get it. nextDenovo v2.4.0To Reproduce (Optional) Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!
Additional context (Optional) Add any other context about the problem here.