[2024-01-25 18:43:05,824] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference
[2024-01-25 18:43:06,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:06,947] [INFO] Task started: Prodigal
[2024-01-25 18:43:06,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9fc30cd-cd55-4b2f-84d1-1483b3f12ea6/GCF_014638745.1_ASM1463874v1_genomic.fna.gz | prodigal -d GCF_014638745.1_ASM1463874v1_genomic.fna/cds.fna -a GCF_014638745.1_ASM1463874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:12,861] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:12,862] [INFO] Task started: HMMsearch
[2024-01-25 18:43:12,862] [INFO] Running command: hmmsearch --tblout GCF_014638745.1_ASM1463874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/reference_markers.hmm GCF_014638745.1_ASM1463874v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:13,087] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:13,088] [INFO] Found 6/6 markers.
[2024-01-25 18:43:13,110] [INFO] Query marker FASTA was written to GCF_014638745.1_ASM1463874v1_genomic.fna/markers.fasta
[2024-01-25 18:43:13,110] [INFO] Task started: Blastn
[2024-01-25 18:43:13,110] [INFO] Running command: blastn -query GCF_014638745.1_ASM1463874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/reference_markers.fasta -out GCF_014638745.1_ASM1463874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:14,032] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:14,034] [INFO] Selected 22 target genomes.
[2024-01-25 18:43:14,035] [INFO] Target genome list was writen to GCF_014638745.1_ASM1463874v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:14,040] [INFO] Task started: fastANI
[2024-01-25 18:43:14,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc30cd-cd55-4b2f-84d1-1483b3f12ea6/GCF_014638745.1_ASM1463874v1_genomic.fna.gz --refList GCF_014638745.1_ASM1463874v1_genomic.fna/target_genomes.txt --output GCF_014638745.1_ASM1463874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:26,976] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:26,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:26,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:26,989] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:26,989] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:26,989] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	81.2982	423	712	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	81.1928	426	712	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	81.0955	445	712	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	80.9971	450	712	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	80.6596	389	712	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	80.6176	405	712	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	80.5163	415	712	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.2952	398	712	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.259	392	712	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	80.1985	376	712	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	80.1675	388	712	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	80.0675	386	712	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	80.0571	372	712	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	79.9449	348	712	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	79.9408	376	712	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	79.889	392	712	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	79.7299	338	712	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	79.6826	379	712	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	79.6346	367	712	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	79.6327	357	712	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.5764	376	712	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	79.2668	294	712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:26,990] [INFO] DFAST Taxonomy check result was written to GCF_014638745.1_ASM1463874v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:26,991] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:26,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:26,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/checkm_data
[2024-01-25 18:43:26,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:27,015] [INFO] Task started: CheckM
[2024-01-25 18:43:27,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638745.1_ASM1463874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638745.1_ASM1463874v1_genomic.fna/checkm_input GCF_014638745.1_ASM1463874v1_genomic.fna/checkm_result
[2024-01-25 18:43:48,602] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:48,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:48,637] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:48,637] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:48,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638745.1_ASM1463874v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:48,638] [INFO] Task started: Blastn
[2024-01-25 18:43:48,638] [INFO] Running command: blastn -query GCF_014638745.1_ASM1463874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ebe1f05-d28b-4023-86ae-7588a9be3a75/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638745.1_ASM1463874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:50,500] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:50,502] [INFO] Selected 17 target genomes.
[2024-01-25 18:43:50,503] [INFO] Target genome list was writen to GCF_014638745.1_ASM1463874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:50,515] [INFO] Task started: fastANI
[2024-01-25 18:43:50,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc30cd-cd55-4b2f-84d1-1483b3f12ea6/GCF_014638745.1_ASM1463874v1_genomic.fna.gz --refList GCF_014638745.1_ASM1463874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638745.1_ASM1463874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:00,710] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:00,720] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:00,720] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014638745.1	s__Arenimonas maotaiensis	100.0	712	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903942465.1	s__Arenimonas sp903942465	82.0405	426	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.54	99.33	0.88	0.87	9	-
GCF_000747075.1	s__Arenimonas malthae	81.2876	424	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	81.1099	444	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	80.9893	452	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	80.6276	439	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	80.551	414	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	80.2572	329	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	80.1592	393	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_008386465.1	s__Arenimonas fontis	80.0386	388	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	80.0131	394	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	79.9966	396	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_007859325.1	s__Luteimonas marina	79.8489	395	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333835.1	s__Silanimonas sp018333835	79.8095	310	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420545.1	s__Arenimonas oryziterrae	79.622	367	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001801685.1	s__Arenimonas sp001801685	79.3174	320	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770795.1	s__Lysobacter_A dokdonensis	79.3056	291	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:00,722] [INFO] GTDB search result was written to GCF_014638745.1_ASM1463874v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:00,722] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:00,725] [INFO] DFAST_QC result json was written to GCF_014638745.1_ASM1463874v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:00,726] [INFO] DFAST_QC completed!
[2024-01-25 18:44:00,726] [INFO] Total running time: 0h0m55s