[2023-06-13 14:58:37,606] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:58:37,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:58:37,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference
[2023-06-13 14:58:38,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:58:38,876] [INFO] Task started: Prodigal
[2023-06-13 14:58:38,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg4402b4df-2578-451c-8c73-e629de677d8d/GCA_022708945.1_ASM2270894v1_genomic.fna.gz | prodigal -d GCA_022708945.1_ASM2270894v1_genomic.fna/cds.fna -a GCA_022708945.1_ASM2270894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:58:45,077] [INFO] Task succeeded: Prodigal
[2023-06-13 14:58:45,078] [INFO] Task started: HMMsearch
[2023-06-13 14:58:45,078] [INFO] Running command: hmmsearch --tblout GCA_022708945.1_ASM2270894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/reference_markers.hmm GCA_022708945.1_ASM2270894v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:58:45,278] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:58:45,279] [INFO] Found 6/6 markers.
[2023-06-13 14:58:45,305] [INFO] Query marker FASTA was written to GCA_022708945.1_ASM2270894v1_genomic.fna/markers.fasta
[2023-06-13 14:58:45,306] [INFO] Task started: Blastn
[2023-06-13 14:58:45,306] [INFO] Running command: blastn -query GCA_022708945.1_ASM2270894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/reference_markers.fasta -out GCA_022708945.1_ASM2270894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:58:45,931] [INFO] Task succeeded: Blastn
[2023-06-13 14:58:45,934] [INFO] Selected 30 target genomes.
[2023-06-13 14:58:45,934] [INFO] Target genome list was writen to GCA_022708945.1_ASM2270894v1_genomic.fna/target_genomes.txt
[2023-06-13 14:58:45,937] [INFO] Task started: fastANI
[2023-06-13 14:58:45,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg4402b4df-2578-451c-8c73-e629de677d8d/GCA_022708945.1_ASM2270894v1_genomic.fna.gz --refList GCA_022708945.1_ASM2270894v1_genomic.fna/target_genomes.txt --output GCA_022708945.1_ASM2270894v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:07,622] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:07,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:07,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:07,641] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:59:07,641] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:59:07,641] [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
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	75.3976	119	888	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.2958	171	888	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.2642	195	888	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	75.2491	56	888	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	75.211	105	888	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	75.203	82	888	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.1107	96	888	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	75.0768	70	888	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	75.0768	70	888	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	75.0391	145	888	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	75.0391	70	888	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.0005	244	888	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	74.9743	99	888	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.935	225	888	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.903	111	888	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.88	224	888	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	74.878	156	888	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	74.8764	210	888	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	74.8619	66	888	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	74.858	116	888	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	74.8235	158	888	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	74.8038	65	888	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.7913	215	888	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:59:07,645] [INFO] DFAST Taxonomy check result was written to GCA_022708945.1_ASM2270894v1_genomic.fna/tc_result.tsv
[2023-06-13 14:59:07,646] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:07,646] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:07,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/checkm_data
[2023-06-13 14:59:07,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:07,679] [INFO] Task started: CheckM
[2023-06-13 14:59:07,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708945.1_ASM2270894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708945.1_ASM2270894v1_genomic.fna/checkm_input GCA_022708945.1_ASM2270894v1_genomic.fna/checkm_result
[2023-06-13 14:59:30,698] [INFO] Task succeeded: CheckM
[2023-06-13 14:59:30,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:59:30,718] [INFO] ===== Completeness check finished =====
[2023-06-13 14:59:30,718] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:59:30,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708945.1_ASM2270894v1_genomic.fna/markers.fasta)
[2023-06-13 14:59:30,719] [INFO] Task started: Blastn
[2023-06-13 14:59:30,719] [INFO] Running command: blastn -query GCA_022708945.1_ASM2270894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df9e805-ef8a-49c6-9b0e-b430d168f08c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708945.1_ASM2270894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:31,679] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:31,683] [INFO] Selected 16 target genomes.
[2023-06-13 14:59:31,683] [INFO] Target genome list was writen to GCA_022708945.1_ASM2270894v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:59:31,689] [INFO] Task started: fastANI
[2023-06-13 14:59:31,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg4402b4df-2578-451c-8c73-e629de677d8d/GCA_022708945.1_ASM2270894v1_genomic.fna.gz --refList GCA_022708945.1_ASM2270894v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708945.1_ASM2270894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:59:43,793] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:43,809] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:59:43,809] [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_012521815.1	s__JAAYLR01 sp012521815	98.6569	728	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	conclusive
GCA_016699405.1	s__JAAYLR01 sp016699405	78.8991	459	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	78.0509	392	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	77.8244	399	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	77.6294	340	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998715.1	s__JAGPDF01 sp017998715	77.4757	266	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057705.1	s__JAGPDF01 sp018057705	77.3224	299	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_003388555.1	s__QQVD01 sp003388555	76.2867	256	888	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009838525.1	s__VXRJ01 sp009838525	75.6755	68	888	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__VXRJ01	95.0	98.98	98.07	0.95	0.93	4	-
GCA_009937385.1	s__QNFN01 sp009937385	75.2017	69	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	75.0309	172	888	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737325.1	s__Sandaracinus amylolyticus	74.9042	275	888	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185305.1	s__JACPNV01 sp016185305	74.8009	63	888	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__JACPNV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:59:43,811] [INFO] GTDB search result was written to GCA_022708945.1_ASM2270894v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:59:43,812] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:59:43,816] [INFO] DFAST_QC result json was written to GCA_022708945.1_ASM2270894v1_genomic.fna/dqc_result.json
[2023-06-13 14:59:43,816] [INFO] DFAST_QC completed!
[2023-06-13 14:59:43,817] [INFO] Total running time: 0h1m6s