[2024-01-24 10:47:06,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference
[2024-01-24 10:47:12,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,831] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d9db429-aad2-4549-85cd-22fa19e645c6/GCF_003610015.1_ASM361001v1_genomic.fna.gz | prodigal -d GCF_003610015.1_ASM361001v1_genomic.fna/cds.fna -a GCF_003610015.1_ASM361001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:22,693] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:22,694] [INFO] Task started: HMMsearch
[2024-01-24 10:47:22,694] [INFO] Running command: hmmsearch --tblout GCF_003610015.1_ASM361001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/reference_markers.hmm GCF_003610015.1_ASM361001v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,955] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,993] [INFO] Query marker FASTA was written to GCF_003610015.1_ASM361001v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,994] [INFO] Task started: Blastn
[2024-01-24 10:47:22,994] [INFO] Running command: blastn -query GCF_003610015.1_ASM361001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/reference_markers.fasta -out GCF_003610015.1_ASM361001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,866] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,877] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:23,877] [INFO] Target genome list was writen to GCF_003610015.1_ASM361001v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,716] [INFO] Task started: fastANI
[2024-01-24 10:47:24,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9db429-aad2-4549-85cd-22fa19e645c6/GCF_003610015.1_ASM361001v1_genomic.fna.gz --refList GCF_003610015.1_ASM361001v1_genomic.fna/target_genomes.txt --output GCF_003610015.1_ASM361001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:39,819] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:39,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:39,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:39,843] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:39,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:39,844] [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
Zymobacter palmae	strain=IAM14233	GCA_003610015.1	33074	33074	type	True	100.0	1008	1008	95	conclusive
Zymobacter palmae	strain=DSM 10491	GCA_000620025.1	33074	33074	type	True	99.9465	961	1008	95	conclusive
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	79.3465	68	1008	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.4771	86	1008	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	78.3122	80	1008	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	77.8496	60	1008	95	below_threshold
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	77.829	129	1008	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	77.5984	61	1008	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	77.4952	74	1008	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	77.3738	79	1008	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	77.3412	75	1008	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.2558	72	1008	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	77.1026	88	1008	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	77.0586	91	1008	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	76.8638	85	1008	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	76.6775	86	1008	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.6576	69	1008	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	76.5374	88	1008	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	76.0104	59	1008	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.9426	66	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:39,850] [INFO] DFAST Taxonomy check result was written to GCF_003610015.1_ASM361001v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:39,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:39,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:39,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/checkm_data
[2024-01-24 10:47:39,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:39,901] [INFO] Task started: CheckM
[2024-01-24 10:47:39,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003610015.1_ASM361001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003610015.1_ASM361001v1_genomic.fna/checkm_input GCF_003610015.1_ASM361001v1_genomic.fna/checkm_result
[2024-01-24 10:48:14,534] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:14,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:14,560] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:14,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:14,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003610015.1_ASM361001v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:14,561] [INFO] Task started: Blastn
[2024-01-24 10:48:14,561] [INFO] Running command: blastn -query GCF_003610015.1_ASM361001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb04ff4-3a47-4c07-807f-5572cd6ea40c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003610015.1_ASM361001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:15,940] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:15,944] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:15,945] [INFO] Target genome list was writen to GCF_003610015.1_ASM361001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:15,996] [INFO] Task started: fastANI
[2024-01-24 10:48:15,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9db429-aad2-4549-85cd-22fa19e645c6/GCF_003610015.1_ASM361001v1_genomic.fna.gz --refList GCF_003610015.1_ASM361001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003610015.1_ASM361001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:34,264] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:34,284] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:34,284] [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_003610015.1	s__Zymobacter palmae	100.0	1005	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Zymobacter	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_012427705.1	s__Halomonas piezotolerans	79.1144	78	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_000196875.2	s__Halomonas elongata	78.3308	90	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCF_001431725.1	s__Halomonas huangheensis	78.2831	80	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001886615.1	s__Halomonas aestuarii	78.2739	83	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155385.1	s__Halomonas massiliensis	78.1827	53	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_013407925.2	s__Pseudomonas_E fluorescens_AP	77.9291	61	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
GCF_001720485.1	s__Cobetia marina	77.7202	128	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_900110265.1	s__Halomonas aquamarina	77.5862	62	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_011742165.1	s__Halomonas bachuensis	77.5349	73	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002925.1	s__Halomonas songnenensis	77.3738	79	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457615.1	s__Pseudomonas aeruginosa	77.3424	66	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_008298015.1	s__Salinicola sp008298015	77.2362	73	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695065.1	s__Salinicola sp002695065	77.129	74	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCA_001577635.1	s__Halomonas_C sp001577635	77.1166	80	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013009075.1	s__Halomonas_B sp013009075	77.1041	89	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	99.96	99.96	1.00	0.99	3	-
GCF_014651775.1	s__Halomonas hamiltonii	77.072	83	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000265245.1	s__Halomonas smyrnensis	77.0586	91	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_000754225.1	s__Cobetia amphilecti	76.911	110	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_900312995.1	s__Kushneria phyllosphaerae	76.8638	85	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	76.7089	85	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902500215.1	s__Halomonas sp902500215	76.6431	69	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633775.1	s__Kushneria sinocarnis	76.5595	87	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900961225.1	s__Halomonas_C sp900961225	76.5101	98	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	76.2141	66	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,286] [INFO] GTDB search result was written to GCF_003610015.1_ASM361001v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:34,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:34,293] [INFO] DFAST_QC result json was written to GCF_003610015.1_ASM361001v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:34,293] [INFO] DFAST_QC completed!
[2024-01-24 10:48:34,294] [INFO] Total running time: 0h1m28s