Closed 000generic closed 4 years ago
moold
commented
4 years ago It seems your system does not include time command, you can use alias time='/usr/bin/time' if your system includes /usr/bin/time, or you can delete the time command in each work shell.
000generic
commented
4 years ago I added the alias alias time='/usr/bin/time'
Running time now produces:
time Usage: /usr/bin/time [-apvV] [-f format] [-o file] [--append] [--verbose] [--portability] [--format=format] [--output=file] [--version] [--quiet] [--help] command [arg...]
Previously this had produced:
time real 0m0.000s user 0m0.000s sys 0m0.000s
but when I now run nextDenovo, I'm getting the same sort of error:
'[INFO] 2020-04-03 13:57:06,433 start... [INFO] 2020-04-03 13:57:06,433 logfile: pid101715.log.info [WARNING] 2020-04-03 13:57:06,433 Re-write workdir [INFO] 2020-04-03 13:57:06,433 options: [INFO] 2020-04-03 13:57:06,433 {'sort_threads': 10, 'nodelist': '', 'rewrite': 1, 'blocksize': '2g', 'job_prefix': 'nextDenovo', 'job_type': 'local', 'minimap2_options_raw': '-x ava-ont -t 8', 'cns_threads': 20, 'sort_mem': '20g', 'seed_cutoff': '7974', 'input_fofn': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/../reads/ont-paradoxus.fasta', 'read_cutoff': '0.5k', 'input_type': 'raw', 'sort_options': '-m 20g -t 10 -k 40', 'parallel_jobs': '60', 'cluster_options': '', 'sge_queue': '', 'ctg_graphdir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/03.ctg_graph', 'pa_correction': '20', 'workdir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir', 'random_round': '20', 'minimap2_threads': (8, 8), 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17', 'cns_aligndir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/02.cns_align', 'seed_cutfiles': '20', 'raw_aligndir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align', 'task': 'all', 'deltmp': 1, 'rerun': 3, 'correction_options': '-p 20 -max_lq_length 10000', 'nextgraph_options': '-a 1'} [INFO] 2020-04-03 13:57:06,433 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir [INFO] 2020-04-03 13:57:06,433 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align [INFO] 2020-04-03 13:57:06,434 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/02.cns_align [INFO] 2020-04-03 13:57:06,434 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/03.ctg_graph [INFO] 2020-04-03 13:57:06,434 analysis tasks done [INFO] 2020-04-03 13:57:06,434 total jobs: 1 [INFO] 2020-04-03 13:57:06,435 Throw jobID:[101716] jobCmd:[/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh] in the local_cycle. [ERROR] 2020-04-03 13:57:06,963 db_split failed: please check the following logs: [ERROR] 2020-04-03 13:57:06,964 /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e
and when I check the indicated log file I get:
less /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e hostname
So it seems like a time value is now showing up - but its a strange one - and the expected file (?) still does not exist.
If necessary, how would I delete the time command in each work shell?
I'm trying to assemble an ~2.2 Gb genome with 50-60x ONT coverage using NextDenovo on a machine with capacity for 48 threads and 1 Tb RAM. My configuration settings are:
[General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 40 input_type = raw input_fofn = input.fofn workdir = 1_rundir
[correct_option] read_cutoff = 0.5k seed_cutoff = 7974 blocksize = 2g pa_correction = 20 seed_cutfiles = 20 sort_options = -m 20g -t 10 -k 40 minimap2_options_raw = -x ava-ont -t 8 correction_options = -p 20
[assemble_option] random_round = 20 minimap2_options_cns = -x ava-ont -t 8 -k17 -w17 nextgraph_options = -a 1
when I run things I get:
(base) ::nextdenovo: bash 02-nextdenovo [INFO] 2020-03-29 16:02:27,359 start... [INFO] 2020-03-29 16:02:27,359 logfile: pid148033.log.info [WARNING] 2020-03-29 16:02:27,359 Re-write workdir [INFO] 2020-03-29 16:02:27,359 options: [INFO] 2020-03-29 16:02:27,359 {'sort_threads': 10, 'nodelist': '', 'rewrite': 1, 'blocksize': '2g', 'job_prefix': 'nextDenovo', 'job_type': 'local', 'minimap2_options_raw': '-x ava-ont -t 8', 'cns_threads': 20, 'sort_mem': '20g', 'seed_cutoff': '7974', 'input_fofn': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/input.fofn', 'read_cutoff': '0.5k', 'input_type': 'raw', 'sort_options': '-m 20g -t 10 -k 40', 'parallel_jobs': '40', 'cluster_options': '', 'sge_queue': '', 'ctg_graphdir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/03.ctg_graph', 'pa_correction': '20', 'workdir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir', 'random_round': '20', 'minimap2_threads': (8, 8), 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17', 'cns_aligndir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/02.cns_align', 'seed_cutfiles': '20', 'raw_aligndir': '/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align', 'task': 'all', 'deltmp': 1, 'rerun': 3, 'correction_options': '-p 20 -max_lq_length 10000', 'nextgraph_options': '-a 1'} [INFO] 2020-03-29 16:02:27,360 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir [INFO] 2020-03-29 16:02:27,360 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align [INFO] 2020-03-29 16:02:27,360 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/02.cns_align [INFO] 2020-03-29 16:02:27,360 mkdir: /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/03.ctg_graph [INFO] 2020-03-29 16:02:27,360 analysis tasks done [INFO] 2020-03-29 16:02:27,360 total jobs: 1 [INFO] 2020-03-29 16:02:27,361 Throw jobID:[148034] jobCmd:[/data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh] in the local_cycle. [ERROR] 2020-03-29 16:02:27,884 db_split failed: please check the following logs: [ERROR] 2020-03-29 16:02:27,884 /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e
and when I check the file I get:
(base) ::nextdenovo: less /data/eedsinger/projects/genomes/idiosepius-paradoxus/assembly/nextdenovo/1_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh.e hostname
Any ideas why this error would be happening? Thank you!