[2024-01-24 14:19:30,662] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:30,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:30,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference
[2024-01-24 14:19:31,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:31,918] [INFO] Task started: Prodigal
[2024-01-24 14:19:31,918] [INFO] Running command: gunzip -c /var/lib/cwl/stga04d98c2-8ef8-45aa-890a-62badabff5ea/GCF_003259155.1_ASM325915v1_genomic.fna.gz | prodigal -d GCF_003259155.1_ASM325915v1_genomic.fna/cds.fna -a GCF_003259155.1_ASM325915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:44,753] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:44,753] [INFO] Task started: HMMsearch
[2024-01-24 14:19:44,753] [INFO] Running command: hmmsearch --tblout GCF_003259155.1_ASM325915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/reference_markers.hmm GCF_003259155.1_ASM325915v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:45,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:45,145] [INFO] Found 6/6 markers.
[2024-01-24 14:19:45,179] [INFO] Query marker FASTA was written to GCF_003259155.1_ASM325915v1_genomic.fna/markers.fasta
[2024-01-24 14:19:45,180] [INFO] Task started: Blastn
[2024-01-24 14:19:45,180] [INFO] Running command: blastn -query GCF_003259155.1_ASM325915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/reference_markers.fasta -out GCF_003259155.1_ASM325915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:46,247] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:46,251] [INFO] Selected 25 target genomes.
[2024-01-24 14:19:46,251] [INFO] Target genome list was writen to GCF_003259155.1_ASM325915v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:46,310] [INFO] Task started: fastANI
[2024-01-24 14:19:46,310] [INFO] Running command: fastANI --query /var/lib/cwl/stga04d98c2-8ef8-45aa-890a-62badabff5ea/GCF_003259155.1_ASM325915v1_genomic.fna.gz --refList GCF_003259155.1_ASM325915v1_genomic.fna/target_genomes.txt --output GCF_003259155.1_ASM325915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:09,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:09,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:09,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:09,746] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:09,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:09,747] [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
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	100.0	1246	1246	95	conclusive
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	77.9089	289	1246	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	77.8522	259	1246	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	77.0991	52	1246	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.927	123	1246	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	76.7107	107	1246	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.657	102	1246	95	below_threshold
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	76.6497	104	1246	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	76.635	121	1246	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.5911	133	1246	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.5755	134	1246	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	76.5568	95	1246	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.4822	87	1246	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.4722	99	1246	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.2853	71	1246	95	below_threshold
Teredinibacter turnerae	strain=T7902	GCA_000379165.1	2426	2426	type	True	76.2486	58	1246	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	76.133	97	1246	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	76.0676	74	1246	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.015	95	1246	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.0072	98	1246	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	75.9137	85	1246	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7236	82	1246	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.7092	85	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:09,756] [INFO] DFAST Taxonomy check result was written to GCF_003259155.1_ASM325915v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:09,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:09,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:09,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/checkm_data
[2024-01-24 14:20:09,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:09,798] [INFO] Task started: CheckM
[2024-01-24 14:20:09,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259155.1_ASM325915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259155.1_ASM325915v1_genomic.fna/checkm_input GCF_003259155.1_ASM325915v1_genomic.fna/checkm_result
[2024-01-24 14:20:49,678] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:49,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:49,700] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:49,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:49,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259155.1_ASM325915v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:49,701] [INFO] Task started: Blastn
[2024-01-24 14:20:49,702] [INFO] Running command: blastn -query GCF_003259155.1_ASM325915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d642b81-82c4-4315-b144-d4f9978d47ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259155.1_ASM325915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:51,035] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:51,038] [INFO] Selected 23 target genomes.
[2024-01-24 14:20:51,038] [INFO] Target genome list was writen to GCF_003259155.1_ASM325915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:51,113] [INFO] Task started: fastANI
[2024-01-24 14:20:51,114] [INFO] Running command: fastANI --query /var/lib/cwl/stga04d98c2-8ef8-45aa-890a-62badabff5ea/GCF_003259155.1_ASM325915v1_genomic.fna.gz --refList GCF_003259155.1_ASM325915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259155.1_ASM325915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:08,428] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:08,451] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:08,452] [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_003259155.1	s__Marinimicrobium_A alkaliphilum	100.0	1246	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423345.1	s__Marinimicrobium agarilyticum	77.894	258	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762925.1	s__Marinimicrobium koreense	77.8811	292	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	77.0171	129	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	76.9246	123	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	76.8989	115	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.7833	106	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	76.6889	120	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766945.1	s__Cellvibrio mixtus_A	76.6819	75	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	76.6699	87	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162135.1	s__Cellvibrio sp002162135	76.6585	143	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183545.1	s__Cellvibrio sp001183545	76.6576	60	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750105.1	s__Microbulbifer aggregans	76.6497	104	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	76.5755	134	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_008064665.1	s__Parahaliea maris	76.518	98	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	76.5149	75	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	76.5061	85	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	76.5054	86	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	76.2356	100	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483365.1	s__Cellvibrio sp002483365	76.2352	56	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	76.1889	86	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCA_012735335.1	s__Pseudomonas_D sp012735335	75.7772	61	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,454] [INFO] GTDB search result was written to GCF_003259155.1_ASM325915v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:08,454] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:08,459] [INFO] DFAST_QC result json was written to GCF_003259155.1_ASM325915v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:08,459] [INFO] DFAST_QC completed!
[2024-01-24 14:21:08,459] [INFO] Total running time: 0h1m38s