[2024-01-25 17:46:35,511] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:35,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:35,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference
[2024-01-25 17:46:36,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:36,646] [INFO] Task started: Prodigal
[2024-01-25 17:46:36,646] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7d4e254-6810-40b0-9f38-c61c889eb5cc/GCF_013315265.1_ASM1331526v1_genomic.fna.gz | prodigal -d GCF_013315265.1_ASM1331526v1_genomic.fna/cds.fna -a GCF_013315265.1_ASM1331526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:47,419] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:47,420] [INFO] Task started: HMMsearch
[2024-01-25 17:46:47,420] [INFO] Running command: hmmsearch --tblout GCF_013315265.1_ASM1331526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/reference_markers.hmm GCF_013315265.1_ASM1331526v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:47,635] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:47,636] [INFO] Found 6/6 markers.
[2024-01-25 17:46:47,681] [INFO] Query marker FASTA was written to GCF_013315265.1_ASM1331526v1_genomic.fna/markers.fasta
[2024-01-25 17:46:47,681] [INFO] Task started: Blastn
[2024-01-25 17:46:47,681] [INFO] Running command: blastn -query GCF_013315265.1_ASM1331526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/reference_markers.fasta -out GCF_013315265.1_ASM1331526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:48,396] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:48,399] [INFO] Selected 32 target genomes.
[2024-01-25 17:46:48,400] [INFO] Target genome list was writen to GCF_013315265.1_ASM1331526v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:48,474] [INFO] Task started: fastANI
[2024-01-25 17:46:48,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7d4e254-6810-40b0-9f38-c61c889eb5cc/GCF_013315265.1_ASM1331526v1_genomic.fna.gz --refList GCF_013315265.1_ASM1331526v1_genomic.fna/target_genomes.txt --output GCF_013315265.1_ASM1331526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:09,444] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:09,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:09,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:09,463] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:47:09,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:47:09,463] [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
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	77.2984	132	1294	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	77.0838	136	1294	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.9703	99	1294	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.9552	127	1294	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.9315	171	1294	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.8706	127	1294	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.848	85	1294	95	below_threshold
Pelagimonas varians	strain=DSM 23678	GCA_003208435.1	696760	696760	type	True	76.8386	102	1294	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.7872	99	1294	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	76.761	122	1294	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.7035	97	1294	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.6887	134	1294	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.6785	133	1294	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.677	101	1294	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.6738	125	1294	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6491	113	1294	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.6387	129	1294	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.6322	102	1294	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.6278	53	1294	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.6243	124	1294	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.6203	96	1294	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.5962	114	1294	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.5182	129	1294	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	76.4969	122	1294	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.4604	82	1294	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.4373	108	1294	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.4345	97	1294	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.4036	128	1294	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.4002	126	1294	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.304	98	1294	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	76.2587	132	1294	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	76.2447	99	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:09,465] [INFO] DFAST Taxonomy check result was written to GCF_013315265.1_ASM1331526v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:09,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:09,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:09,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/checkm_data
[2024-01-25 17:47:09,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:09,508] [INFO] Task started: CheckM
[2024-01-25 17:47:09,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013315265.1_ASM1331526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013315265.1_ASM1331526v1_genomic.fna/checkm_input GCF_013315265.1_ASM1331526v1_genomic.fna/checkm_result
[2024-01-25 17:47:43,881] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:43,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:43,902] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:43,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:43,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013315265.1_ASM1331526v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:43,902] [INFO] Task started: Blastn
[2024-01-25 17:47:43,903] [INFO] Running command: blastn -query GCF_013315265.1_ASM1331526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb50ef1f4-bab3-44e4-9341-e954ce9b9083/dqc_reference/reference_markers_gtdb.fasta -out GCF_013315265.1_ASM1331526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:45,257] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:45,260] [INFO] Selected 22 target genomes.
[2024-01-25 17:47:45,260] [INFO] Target genome list was writen to GCF_013315265.1_ASM1331526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:45,279] [INFO] Task started: fastANI
[2024-01-25 17:47:45,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7d4e254-6810-40b0-9f38-c61c889eb5cc/GCF_013315265.1_ASM1331526v1_genomic.fna.gz --refList GCF_013315265.1_ASM1331526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013315265.1_ASM1331526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:01,094] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:01,106] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:01,107] [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_013315265.1	s__Sulfitobacter_F algicola	100.0	1292	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017592335.1	s__Sulfitobacter_F sp017592335	82.1927	459	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154785.2	s__Roseobacter litoralis	77.3203	131	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.963	135	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.9329	172	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208435.1	s__Pelagimonas varians	76.8591	103	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.8338	153	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.7912	100	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.7561	134	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000158135.1	s__Ruegeria sp000158135	76.7414	130	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.717	146	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669325.1	s__Roseovarius bejariae	76.6738	125	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	76.6401	126	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_004799325.1	s__Thalassobius vesicularis	76.5376	125	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364805.1	s__Pelagimonas phthalicica	76.5182	129	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCF_000671395.1	s__Actibacterium atlanticum	76.4802	123	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172335.1	s__Roseovarius albus	76.4442	109	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005518135.1	s__Shimia litoralis	76.4396	98	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	76.4036	128	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990645.1	s__Shimia sediminis	76.2587	132	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	76.2447	99	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:01,108] [INFO] GTDB search result was written to GCF_013315265.1_ASM1331526v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:01,109] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:01,113] [INFO] DFAST_QC result json was written to GCF_013315265.1_ASM1331526v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:01,113] [INFO] DFAST_QC completed!
[2024-01-25 17:48:01,113] [INFO] Total running time: 0h1m26s