db_stat failed - Githubissues

Describe the bug Hello, running nextdenovo on my PacBio HiFi dataset using the following configuration file

gives the following error message: nextDenovo Rotaria_rotatoria.inputHiFi.conf --log Rotaria_rotatoria.inputHiFi.conf.log [17184 INFO] 2022-12-15 10:00:59 NextDenovo start... [17184 INFO] 2022-12-15 10:00:59 version:v2.5.0 logfile:pid17184.Rotaria_rotatoria.inputHiFi.conf.log [17184 WARNING] 2022-12-15 10:00:59 Re-write workdir [17184 WARNING] 2022-12-15 10:00:59 Change task "all" to "assemble", becasue the input_type is "corrected" [17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir [17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align [17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/02.cns_align [17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/03.ctg_graph [17184 INFO] 2022-12-15 10:01:04 Total jobs: 1 [17184 INFO] 2022-12-15 10:01:04 Submitted jobID:[17185] jobCmd:[/mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle. [17185 CRITICAL] 2022-12-15 10:01:04 Command '/bin/sh /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 1, error info: . Traceback (most recent call last): File "/mnt/sdc1/Alex/software/NextDenovo/nextDenovo", line 850, in main(args) File "/mnt/sdc1/Alex/software/NextDenovo/nextDenovo", line 594, in main task.run.start() File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 347, in start self._start() File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 371, in _start self.submit(job) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/taskcontrol.py", line 255, in submit , stdout, _ = self.run(job.cmd) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 291, in run log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr)) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1219, in critical self._log(CRITICAL, msg, args, **kwargs) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1293, in _log self.handle(record) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1303, in handle self.callHandlers(record) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1343, in callHandlers hdlr.handle(record) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 766, in handle self.emit(record) File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/sh /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 1, error info: . [17184 ERROR] 2022-12-15 10:01:10 db_stat failed: please check the following logs: [17184 ERROR] 2022-12-15 10:01:10 /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e

Content of nextDenovo.sh.e: hostname hostname cd /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1 cd /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1 time /mnt/sdc1/Alex/software/NextDenovo/bin/seq_stat -f 10k -g 180m -d 30 -a -o /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/input.reads.stat /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.inputHiFi.fofn time /mnt/sdc1/Alex/software/NextDenovo/bin/seq_stat -f 10k -g 180m -d 30 -a -o /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/input.reads.stat /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.inputHiFi.fofn Error! /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/02.FILTLONG/Rotaria_rotatoria.PacBio_HiFi.m64279e_221025_110133.fastq.gz does not exist!Command exited with non-zero status 1 0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 1932maxresident)k 0inputs+0outputs (0major+80minor)pagefaults 0swaps

Genome characteristics The genome size should be aroung 180-200Mb (haploid) although we are not sure

Input data The input length distribution is the following Types Count (#) Length (bp) N10 6415 14208 N20 13658 13204 N30 21350 12547 N40 29407 12028 N50 37786 11589 N60 46465 11210 N70 55425 10875 N80 64655 10562 N90 74151 10270

Types Count (#) Bases (bp) Depth (X) Raw 83911 989053808 4.95 Filtered 0 0 0.00 Clean 83911 989053808 4.95

Config file [General]

job_type = local job_prefix = nextDenovo task = all rewrite = yes deltmp = yes rerun = 3 parallel_jobs = 10 input_type = raw input_fofn = Rotaria_rotatoria.inputHiFi.10000.90.fofn workdir = /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.10000.90.workdir [correct_option] read_cutoff = 10k seed_cutoff = 10001 seed_depth = 45 read_type=hifi genome_size = 200M # estimated genome size blocksize = 1g pa_correction = 10 seed_cutfiles = 2 sort_options = -m 5g -t 2 -k 40 minimap2_options_raw = -x ava-hifi -t 2 correction_options = -p 15 [assemble_option] random_round = 10 minimap2_options_cns = -x ava-hifi -t 2 -k17 -w17 nextgraph_options = -a 1

Operating system Distributor ID: Ubuntu Description: Ubuntu 18.10 Release: 18.10 Codename: cosmic

GCC gcc version 8.3.0 (Ubuntu 8.3.0-6ubuntu1~18.10.1)

Python Python 2.7.15

NextDenovo nextDenovo v2.5.0

Any help would be appreciated thanks Alex

Nextomics / NextDenovo

db_stat failed #158