[2023-06-29 09:02:18,453] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:18,455] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:18,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference
[2023-06-29 09:02:19,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:19,766] [INFO] Task started: Prodigal
[2023-06-29 09:02:19,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgafb79e6f-b242-45df-8f0b-a0a773b05ad4/GCA_020849115.1_ASM2084911v1_genomic.fna.gz | prodigal -d GCA_020849115.1_ASM2084911v1_genomic.fna/cds.fna -a GCA_020849115.1_ASM2084911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:43,973] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:43,973] [INFO] Task started: HMMsearch
[2023-06-29 09:02:43,974] [INFO] Running command: hmmsearch --tblout GCA_020849115.1_ASM2084911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/reference_markers.hmm GCA_020849115.1_ASM2084911v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:44,367] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:44,368] [INFO] Found 6/6 markers.
[2023-06-29 09:02:44,440] [INFO] Query marker FASTA was written to GCA_020849115.1_ASM2084911v1_genomic.fna/markers.fasta
[2023-06-29 09:02:44,441] [INFO] Task started: Blastn
[2023-06-29 09:02:44,441] [INFO] Running command: blastn -query GCA_020849115.1_ASM2084911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/reference_markers.fasta -out GCA_020849115.1_ASM2084911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:45,204] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:45,208] [INFO] Selected 34 target genomes.
[2023-06-29 09:02:45,208] [INFO] Target genome list was writen to GCA_020849115.1_ASM2084911v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:45,232] [INFO] Task started: fastANI
[2023-06-29 09:02:45,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb79e6f-b242-45df-8f0b-a0a773b05ad4/GCA_020849115.1_ASM2084911v1_genomic.fna.gz --refList GCA_020849115.1_ASM2084911v1_genomic.fna/target_genomes.txt --output GCA_020849115.1_ASM2084911v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:19,193] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:19,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:19,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:19,231] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:19,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:03:19,231] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.5897	548	2673	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.4128	354	2673	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.398	513	2673	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.3754	324	2673	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.3452	511	2673	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	75.2674	89	2673	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	75.1832	93	2673	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.088	590	2673	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	75.0336	208	2673	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	75.0197	166	2673	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.0125	212	2673	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.006	229	2673	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	74.9505	182	2673	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9334	275	2673	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.9264	249	2673	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.9212	187	2673	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.9205	201	2673	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.9165	209	2673	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.9105	255	2673	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	74.9101	187	2673	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	74.9041	194	2673	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	74.8979	220	2673	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.8947	188	2673	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	74.8535	188	2673	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	74.8534	190	2673	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	74.8531	222	2673	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	74.8355	153	2673	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	74.792	198	2673	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	74.7756	129	2673	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	74.7749	105	2673	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	74.7689	130	2673	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	74.7688	107	2673	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	74.7636	260	2673	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	74.6523	126	2673	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:03:19,233] [INFO] DFAST Taxonomy check result was written to GCA_020849115.1_ASM2084911v1_genomic.fna/tc_result.tsv
[2023-06-29 09:03:19,234] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:19,234] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:19,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/checkm_data
[2023-06-29 09:03:19,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:19,312] [INFO] Task started: CheckM
[2023-06-29 09:03:19,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020849115.1_ASM2084911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020849115.1_ASM2084911v1_genomic.fna/checkm_input GCA_020849115.1_ASM2084911v1_genomic.fna/checkm_result
[2023-06-29 09:05:02,827] [INFO] Task succeeded: CheckM
[2023-06-29 09:05:02,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:05:02,855] [INFO] ===== Completeness check finished =====
[2023-06-29 09:05:02,855] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:05:02,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020849115.1_ASM2084911v1_genomic.fna/markers.fasta)
[2023-06-29 09:05:02,856] [INFO] Task started: Blastn
[2023-06-29 09:05:02,856] [INFO] Running command: blastn -query GCA_020849115.1_ASM2084911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcca6710-7211-436f-9dd2-d42e81182d08/dqc_reference/reference_markers_gtdb.fasta -out GCA_020849115.1_ASM2084911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:05:04,027] [INFO] Task succeeded: Blastn
[2023-06-29 09:05:04,032] [INFO] Selected 16 target genomes.
[2023-06-29 09:05:04,032] [INFO] Target genome list was writen to GCA_020849115.1_ASM2084911v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:05:04,041] [INFO] Task started: fastANI
[2023-06-29 09:05:04,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb79e6f-b242-45df-8f0b-a0a773b05ad4/GCA_020849115.1_ASM2084911v1_genomic.fna.gz --refList GCA_020849115.1_ASM2084911v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020849115.1_ASM2084911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:05:29,069] [INFO] Task succeeded: fastANI
[2023-06-29 09:05:29,086] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:05:29,087] [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
GCA_016191785.1	s__JADJKB01 sp016191785	86.1768	2046	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075635.1	s__JADJKB01 sp015075635	81.1972	1772	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	96.31	96.31	0.86	0.86	2	-
GCA_016706225.1	s__JADJKB01 sp016706225	78.956	1306	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514535.1	s__NIC37A-2 sp012514535	76.3307	285	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__NIC37A-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193285.1	s__PMG-095 sp004193285	76.2421	384	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__PMG-095	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.104	400	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	75.6188	379	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	75.6082	543	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.5535	560	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	75.5185	555	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
GCA_016933275.1	s__JAFGBI01 sp016933275	75.4671	277	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAFGBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899635.1	s__Labilithrix sp001899635	75.4503	399	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	75.3279	623	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	75.2814	732	2673	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_003242475.1	s__ZC4RG40 sp003242475	75.1573	114	2673	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	74.8604	200	2673	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-29 09:05:29,089] [INFO] GTDB search result was written to GCA_020849115.1_ASM2084911v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:05:29,090] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:05:29,099] [INFO] DFAST_QC result json was written to GCA_020849115.1_ASM2084911v1_genomic.fna/dqc_result.json
[2023-06-29 09:05:29,099] [INFO] DFAST_QC completed!
[2023-06-29 09:05:29,100] [INFO] Total running time: 0h3m11s