[2024-01-24 13:49:55,147] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference
[2024-01-24 13:49:56,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,374] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg6506f420-54e0-4855-aab3-5c28bab24fc7/GCF_003015185.1_ASM301518v1_genomic.fna.gz | prodigal -d GCF_003015185.1_ASM301518v1_genomic.fna/cds.fna -a GCF_003015185.1_ASM301518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:19,437] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:19,438] [INFO] Task started: HMMsearch
[2024-01-24 13:50:19,438] [INFO] Running command: hmmsearch --tblout GCF_003015185.1_ASM301518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/reference_markers.hmm GCF_003015185.1_ASM301518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:19,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:19,769] [INFO] Found 6/6 markers.
[2024-01-24 13:50:19,825] [INFO] Query marker FASTA was written to GCF_003015185.1_ASM301518v1_genomic.fna/markers.fasta
[2024-01-24 13:50:19,826] [INFO] Task started: Blastn
[2024-01-24 13:50:19,826] [INFO] Running command: blastn -query GCF_003015185.1_ASM301518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/reference_markers.fasta -out GCF_003015185.1_ASM301518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:20,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:20,583] [INFO] Selected 32 target genomes.
[2024-01-24 13:50:20,583] [INFO] Target genome list was writen to GCF_003015185.1_ASM301518v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:20,594] [INFO] Task started: fastANI
[2024-01-24 13:50:20,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg6506f420-54e0-4855-aab3-5c28bab24fc7/GCF_003015185.1_ASM301518v1_genomic.fna.gz --refList GCF_003015185.1_ASM301518v1_genomic.fna/target_genomes.txt --output GCF_003015185.1_ASM301518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:43,437] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:43,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:43,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:43,462] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:43,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:43,462] [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
Ahniella affigens	strain=D13	GCA_003015185.1	2021234	2021234	type	True	100.0	2039	2039	95	conclusive
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	77.4435	111	2039	95	below_threshold
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	77.3402	120	2039	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	77.2012	130	2039	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.0977	81	2039	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	77.0889	92	2039	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.0832	110	2039	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	77.0812	141	2039	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.0804	100	2039	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	77.0791	94	2039	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	77.0467	102	2039	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	77.01	99	2039	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.9385	134	2039	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.9288	100	2039	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	76.8846	88	2039	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.8489	176	2039	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.8401	134	2039	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	76.788	134	2039	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.7851	124	2039	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.6956	129	2039	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	76.6345	104	2039	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	76.6162	146	2039	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	76.5907	98	2039	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	76.5551	125	2039	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	76.5536	121	2039	95	below_threshold
Lysobacter pythonis	strain=4284/11	GCA_003697345.1	2483112	2483112	type	True	76.4684	86	2039	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.2839	132	2039	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.2769	99	2039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:43,464] [INFO] DFAST Taxonomy check result was written to GCF_003015185.1_ASM301518v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:43,465] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:43,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:43,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/checkm_data
[2024-01-24 13:50:43,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:43,527] [INFO] Task started: CheckM
[2024-01-24 13:50:43,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003015185.1_ASM301518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003015185.1_ASM301518v1_genomic.fna/checkm_input GCF_003015185.1_ASM301518v1_genomic.fna/checkm_result
[2024-01-24 13:51:58,968] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:58,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:58,992] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:58,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:58,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003015185.1_ASM301518v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:58,993] [INFO] Task started: Blastn
[2024-01-24 13:51:58,993] [INFO] Running command: blastn -query GCF_003015185.1_ASM301518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85778fc0-9750-48a4-b88d-b955c1d59998/dqc_reference/reference_markers_gtdb.fasta -out GCF_003015185.1_ASM301518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:00,069] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:00,074] [INFO] Selected 25 target genomes.
[2024-01-24 13:52:00,074] [INFO] Target genome list was writen to GCF_003015185.1_ASM301518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:00,142] [INFO] Task started: fastANI
[2024-01-24 13:52:00,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg6506f420-54e0-4855-aab3-5c28bab24fc7/GCF_003015185.1_ASM301518v1_genomic.fna.gz --refList GCF_003015185.1_ASM301518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003015185.1_ASM301518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:18,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:18,946] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:18,947] [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_003015185.1	s__Ahniella affigens	100.0	2039	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__Ahniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016712105.1	s__Ahniella sp016712105	78.1311	442	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__Ahniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721845.1	s__JADKHK01 sp016721845	77.4784	244	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.21	98.90	0.96	0.94	3	-
GCA_016703225.1	s__JADKHK01 sp016703225	77.1904	233	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.05	99.05	0.90	0.90	2	-
GCA_016182785.1	s__JADKHK01 sp016182785	77.1032	221	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	77.0889	92	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014863405.1	s__Dyella_B sp014863405	77.0851	110	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	77.0804	100	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708465.1	s__JADKHK01 sp016708465	77.0641	167	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.43	99.22	0.94	0.94	3	-
GCF_016904945.1	s__Dyella_B mobilis	77.01	99	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240485.1	s__Rudaea sp018240485	76.9968	81	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rudaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847975.1	s__Lysobacter sp018847975	76.8717	138	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	76.7362	150	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114495.1	s__Dyella sp900114495	76.7274	110	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	76.717	166	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725155.1	s__Tahibacter sp001725155	76.6428	205	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCF_004342425.1	s__Dokdonella_A fugitiva	76.6162	146	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCF_012275375.1	s__Dyella sp012275375	76.6043	125	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCA_005877675.1	s__Rudaea sp005877675	76.4836	115	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rudaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697345.1	s__Lysobacter_B pythonis	76.4684	86	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	76.3565	117	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002785585.1	s__0-14-3-00-62-12 sp002785585	76.2198	100	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__0-14-3-00-62-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240765.1	s__Rudaea sp018240765	76.0127	78	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rudaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:18,948] [INFO] GTDB search result was written to GCF_003015185.1_ASM301518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:18,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:18,956] [INFO] DFAST_QC result json was written to GCF_003015185.1_ASM301518v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:18,957] [INFO] DFAST_QC completed!
[2024-01-24 13:52:18,957] [INFO] Total running time: 0h2m24s