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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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test run is finished, but assembly file is none #15

Closed bioone closed 4 years ago

bioone commented 4 years ago

I install the software and run the test.The log file is below.

[INFO] 2019-10-19 06:47:40,949 start...
[INFO] 2019-10-19 06:47:40,950 logfile: pid28989.log.info
[WARNING] 2019-10-19 06:47:40,951 Re-write workdir
[INFO] 2019-10-19 06:47:40,952 options:
[INFO] 2019-10-19 06:47:40,952 {'sort_threads': 2, 'nodelist': '', 'rewrite': 1, 'blocksize': '1g', 'job_prefix': 'nextDenovo', 'job_type': 'local', 'minimap2_options_raw': '-x ava-ont -t 8', 'cns_threads': 15, 'sort_mem': '1g', 'seed_cutoff': '32000', 'input_fofn': '/data/software/NextDenovo/test_data/./input.fofn', 'read_cutoff': '1k', 'input_type': 'raw', 'sort_options': '-m 1g -t 2 -k 50', 'parallel_jobs': '2', 'cluster_options': '', 'ctg_graphdir': '/data/software/NextDenovo/test_data/./01_rundir/03.ctg_graph', 'pa_correction': '2', 'workdir': '/data/software/NextDenovo/test_data/./01_rundir', 'random_round': '10', 'minimap2_threads': (8, 8), 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17', 'cns_aligndir': '/data/software/NextDenovo/test_data/./01_rundir/02.cns_align', 'seed_cutfiles': '2', 'raw_aligndir': '/data/software/NextDenovo/test_data/./01_rundir/01.raw_align', 'task': 'all', 'deltmp': 1, 'rerun': 3, 'correction_options': '-p 15 -max_lq_length 10000', 'nextgraph_options': '-a 1'}
[INFO] 2019-10-19 06:47:40,952 mkdir: /data/software/NextDenovo/test_data/./01_rundir
[INFO] 2019-10-19 06:47:40,953 mkdir: /data/software/NextDenovo/test_data/./01_rundir/01.raw_align
[INFO] 2019-10-19 06:47:40,953 mkdir: /data/software/NextDenovo/test_data/./01_rundir/02.cns_align
[INFO] 2019-10-19 06:47:40,953 mkdir: /data/software/NextDenovo/test_data/./01_rundir/03.ctg_graph
[INFO] 2019-10-19 06:47:40,954 analysis tasks done
[INFO] 2019-10-19 06:47:40,955 total jobs: 1
[INFO] 2019-10-19 06:47:40,956 Throw jobID:[29002] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/01.db_split.sh.work/db_split0/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:41,635 db_split done
[INFO] 2019-10-19 06:47:41,636 analysis tasks done
[INFO] 2019-10-19 06:47:41,637 total jobs: 5
[INFO] 2019-10-19 06:47:41,638 Throw jobID:[29011] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:42,140 Throw jobID:[29017] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align1/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:44,229 Throw jobID:[29074] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align2/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:45,404 Throw jobID:[29099] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align3/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:47,565 Throw jobID:[29141] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align4/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:51,040 raw_align done
[INFO] 2019-10-19 06:47:51,042 analysis tasks done
[INFO] 2019-10-19 06:47:51,043 total jobs: 2
[INFO] 2019-10-19 06:47:51,045 Throw jobID:[29206] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align0/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:51,547 Throw jobID:[29212] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align1/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:54,208 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align2/input.seed.002.2bit.2.ovl
[INFO] 2019-10-19 06:47:54,208 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align3/input.seed.002.2bit.3.ovl
[INFO] 2019-10-19 06:47:54,208 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align4/input.seed.002.2bit.4.ovl
[INFO] 2019-10-19 06:47:54,209 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align0/input.seed.001.2bit.0.ovl
[INFO] 2019-10-19 06:47:54,209 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align1/input.seed.001.2bit.1.ovl
[INFO] 2019-10-19 06:47:54,209 remove temporary result: /data/software/NextDenovo/test_data/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align2/input.seed.001.2bit.2.ovl
[INFO] 2019-10-19 06:47:54,213 sort_align done
[INFO] 2019-10-19 06:47:54,214 analysis tasks done
[INFO] 2019-10-19 06:47:54,216 total jobs: 2
[INFO] 2019-10-19 06:47:54,217 Throw jobID:[29254] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns0/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:47:54,719 Throw jobID:[29278] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns1/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:01,304 get_cns done
[INFO] 2019-10-19 06:48:01,304 cns finished, and final corrected reads file:
[INFO] 2019-10-19 06:48:01,304  /data/software/NextDenovo/test_data/./01_rundir/02.cns_align/01.get_cns.sh.work/get_cns*/cns.fasta
[INFO] 2019-10-19 06:48:01,305 analysis tasks done
[INFO] 2019-10-19 06:48:01,306 total jobs: 3
[INFO] 2019-10-19 06:48:01,307 Throw jobID:[29330] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align0/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:01,809 Throw jobID:[29337] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align1/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:04,389 Throw jobID:[29388] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align2/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:07,400 cns_align done
[INFO] 2019-10-19 06:48:07,401 analysis tasks done
[INFO] 2019-10-19 06:48:07,403 total jobs: 11
[INFO] 2019-10-19 06:48:07,404 Throw jobID:[29442] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph00/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:07,906 Throw jobID:[29448] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph01/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:08,610 Throw jobID:[29456] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph02/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:09,112 Throw jobID:[29462] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph03/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:09,762 Throw jobID:[29481] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph04/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:10,282 Throw jobID:[29500] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph05/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:11,198 Throw jobID:[29507] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph06/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:11,907 Throw jobID:[29514] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph07/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:12,656 Throw jobID:[29522] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph08/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:13,158 Throw jobID:[29528] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph09/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:13,826 Throw jobID:[29548] jobCmd:[/data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph10/nextDenovo.sh] in the local_cycle.
[INFO] 2019-10-19 06:48:15,029 ctg_graph done
[INFO] 2019-10-19 06:48:15,030 nextDenovo finished
[INFO] 2019-10-19 06:48:15,030 final assembly file:
[INFO] 2019-10-19 06:48:15,030  /data/software/NextDenovo/test_data/./01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph*/nextgraph.assembly.contig.fasta
[INFO] 2019-10-19 06:48:15,031 final stat files:
[INFO] 2019-10-19 06:48:15,031  /data/software/NextDenovo/test_data/./01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph*/nextDenovo.sh.e

But the assembly file is only in /data/software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph00/,and file is empty. Is this right? My linux system is ubuntu18.04!

moold commented 4 years ago

Yes, it is right. To minimize the size of the installation package, the test data only includes few of reads, which may not be enough to assemble depending on different parameters. If there is an error, the log will show the detail of this error.