Unable to run NextDeVovo on the test data

Describe the bug I am trying to teach myself how to use NextDenovo. I follow the instructions on the installation guide and when I run the test data, it immediately runs into an error. I tried downloading the tutorial data as well and get the same error. I'm not sure what's happening that I can't run the code on even the test data that was supplied with it. Thanks in advance for your help!

Error message blackmonlab@blackmonlab-M-CLASS:~/Desktop/Priscilla/NextDenovo$ ./nextDenovo test_data/run.cfg py -3 [54320 INFO] 2023-01-27 11:46:55 NextDenovo start... [54320 INFO] 2023-01-27 11:46:55 version:v2.5.0 logfile:pid54320.log.info [54320 WARNING] 2023-01-27 11:46:55 Re-write workdir [54320 INFO] 2023-01-27 11:46:55 skip mkdir: /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/./01_rundir [54320 INFO] 2023-01-27 11:46:55 skip mkdir: /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/./01_rundir/01.raw_align [54320 INFO] 2023-01-27 11:46:55 skip mkdir: /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/./01_rundir/02.cns_align [54320 INFO] 2023-01-27 11:46:55 skip mkdir: /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/./01_rundir/03.ctg_graph [54320 INFO] 2023-01-27 11:47:00 Total jobs: 1 [54320 INFO] 2023-01-27 11:47:00 Submitted jobID:[54321] jobCmd:[/home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle. [54321 CRITICAL] 2023-01-27 11:47:00 Command '/bin/sh /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 2, error info: . Traceback (most recent call last): File "./nextDenovo", line 850, in main(args) File "./nextDenovo", line 594, in main task.run.start() File "/home/blackmonlab/.local/lib/python2.7/site-packages/paralleltask/task_control.py", line 348, in start self._start() File "/home/blackmonlab/.local/lib/python2.7/site-packages/paralleltask/task_control.py", line 372, in _start self.submit(job) File "/home/blackmonlab/.local/lib/python2.7/site-packages/paralleltask/taskcontrol.py", line 252, in submit , stdout, _ = self.run(job.cmd) File "/home/blackmonlab/.local/lib/python2.7/site-packages/paralleltask/task_control.py", line 292, in run log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr)) File "/usr/lib/python2.7/logging/init.py", line 1219, in critical self._log(CRITICAL, msg, args, **kwargs) File "/usr/lib/python2.7/logging/init.py", line 1293, in _log self.handle(record) File "/usr/lib/python2.7/logging/init.py", line 1303, in handle self.callHandlers(record) File "/usr/lib/python2.7/logging/init.py", line 1343, in callHandlers hdlr.handle(record) File "/usr/lib/python2.7/logging/init.py", line 766, in handle self.emit(record) File "/home/blackmonlab/.local/lib/python2.7/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/sh /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 2, error info: . [54320 ERROR] 2023-01-27 11:47:06 db_stat failed: please check the following logs: [54320 ERROR] 2023-01-27 11:47:06 /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e

When I open this file, it says: /home/blackmonlab/Desktop/Priscilla/NextDenovo/test_data/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh: 2: set: Illegal option -o pipefail

Genome characteristics original test_data

Input data o.g. test data file

Config file [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 2 input_type = raw read_type = clr input_fofn = ./input.fofn workdir = ./01_rundir

[correct_option] read_cutoff = 1k genome_size = 308161 pa_correction = 2 sort_options = -m 1g -t 2 minimap2_options_raw = -t 8 correction_options = -p 15

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

Operating system No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.6 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 2.7.17

NextDenovo What version of NextDenovo are you using? nextDenovo v2.5.0

To 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) I tried using python 3 as well with no luck in moving past this error

Nextomics / NextDenovo

Unable to run NextDeVovo on the test data #161