[2024-01-24 15:27:41,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9c0a658-005b-4ae5-a0a3-dba658bc42d1/GCF_003990645.1_ASM399064v1_genomic.fna.gz | prodigal -d GCF_003990645.1_ASM399064v1_genomic.fna/cds.fna -a GCF_003990645.1_ASM399064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:58,081] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:58,081] [INFO] Task started: HMMsearch
[2024-01-24 15:27:58,082] [INFO] Running command: hmmsearch --tblout GCF_003990645.1_ASM399064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/reference_markers.hmm GCF_003990645.1_ASM399064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:58,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:58,370] [INFO] Found 6/6 markers.
[2024-01-24 15:27:58,416] [INFO] Query marker FASTA was written to GCF_003990645.1_ASM399064v1_genomic.fna/markers.fasta
[2024-01-24 15:27:58,416] [INFO] Task started: Blastn
[2024-01-24 15:27:58,417] [INFO] Running command: blastn -query GCF_003990645.1_ASM399064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/reference_markers.fasta -out GCF_003990645.1_ASM399064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:59,201] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:59,205] [INFO] Selected 24 target genomes.
[2024-01-24 15:27:59,206] [INFO] Target genome list was writen to GCF_003990645.1_ASM399064v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:59,217] [INFO] Task started: fastANI
[2024-01-24 15:27:59,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c0a658-005b-4ae5-a0a3-dba658bc42d1/GCF_003990645.1_ASM399064v1_genomic.fna.gz --refList GCF_003990645.1_ASM399064v1_genomic.fna/target_genomes.txt --output GCF_003990645.1_ASM399064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:17,082] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:17,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:17,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:17,105] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:17,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:17,105] [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
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	100.0	1414	1417	95	conclusive
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	79.2216	559	1417	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	78.4198	384	1417	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.3664	405	1417	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2981	450	1417	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.1506	396	1417	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.0736	383	1417	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.01	346	1417	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.9624	319	1417	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9613	352	1417	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.9524	320	1417	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.9044	371	1417	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.8757	355	1417	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8749	335	1417	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.8569	317	1417	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	77.6595	249	1417	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.5861	301	1417	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.5833	276	1417	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5201	242	1417	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.5137	307	1417	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.1471	152	1417	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.964	215	1417	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.8114	210	1417	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.6634	196	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:17,108] [INFO] DFAST Taxonomy check result was written to GCF_003990645.1_ASM399064v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:17,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:17,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:17,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/checkm_data
[2024-01-24 15:28:17,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:17,154] [INFO] Task started: CheckM
[2024-01-24 15:28:17,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990645.1_ASM399064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990645.1_ASM399064v1_genomic.fna/checkm_input GCF_003990645.1_ASM399064v1_genomic.fna/checkm_result
[2024-01-24 15:29:00,931] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:00,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:00,956] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:00,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:00,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990645.1_ASM399064v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:00,957] [INFO] Task started: Blastn
[2024-01-24 15:29:00,958] [INFO] Running command: blastn -query GCF_003990645.1_ASM399064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf66506d5-0ed0-412f-807d-d996e3a4857f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990645.1_ASM399064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:02,188] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:02,194] [INFO] Selected 24 target genomes.
[2024-01-24 15:29:02,195] [INFO] Target genome list was writen to GCF_003990645.1_ASM399064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:02,212] [INFO] Task started: fastANI
[2024-01-24 15:29:02,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c0a658-005b-4ae5-a0a3-dba658bc42d1/GCF_003990645.1_ASM399064v1_genomic.fna.gz --refList GCF_003990645.1_ASM399064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990645.1_ASM399064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:22,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:22,370] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:22,371] [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_003990645.1	s__Shimia sediminis	100.0	1414	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114635.1	s__Shimia aestuarii	79.5274	576	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142085.1	s__Shimia gijangensis	79.2265	559	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	78.8251	520	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_016888515.1	s__Shimia_A biformata	78.8175	517	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	78.6183	429	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	78.4844	416	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	78.3609	405	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.2764	386	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017743735.1	s__Shimia sp017743735	78.2638	385	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_009857745.1	s__Thalassobius mangrovi	78.1636	393	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.0941	326	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	78.0774	382	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	78.0633	451	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744095.1	s__Shimia sp017744095	78.0253	330	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.0098	360	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743975.1	s__Ruegeria sp017743975	77.9895	302	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458175.1	s__Shimia marina	77.9615	319	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.8627	355	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_002708925.1	s__Thalassobius sp002708925	77.8073	304	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_013032095.1	s__Ruegeria atlantica_E	77.7497	309	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030265.1	s__Ruegeria arenilitoris_E	77.6773	252	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.5833	276	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_000590925.1	s__Roseicyclus elongatus	77.5339	238	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:22,372] [INFO] GTDB search result was written to GCF_003990645.1_ASM399064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:22,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:22,378] [INFO] DFAST_QC result json was written to GCF_003990645.1_ASM399064v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:22,378] [INFO] DFAST_QC completed!
[2024-01-24 15:29:22,378] [INFO] Total running time: 0h1m41s