[2023-06-17 18:03:39,111] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:03:39,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:03:39,114] [INFO] DQC Reference Directory: /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference
[2023-06-17 18:03:40,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:03:40,262] [INFO] Task started: Prodigal
[2023-06-17 18:03:40,262] [INFO] Running command: gunzip -c /var/lib/cwl/stga88d78a6-c1d5-4203-9fac-46a9f0348db5/GCA_003482965.1_ASM348296v1_genomic.fna.gz | prodigal -d GCA_003482965.1_ASM348296v1_genomic.fna/cds.fna -a GCA_003482965.1_ASM348296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:03:45,878] [INFO] Task succeeded: Prodigal
[2023-06-17 18:03:45,878] [INFO] Task started: HMMsearch
[2023-06-17 18:03:45,878] [INFO] Running command: hmmsearch --tblout GCA_003482965.1_ASM348296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/reference_markers.hmm GCA_003482965.1_ASM348296v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:03:46,064] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:03:46,066] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga88d78a6-c1d5-4203-9fac-46a9f0348db5/GCA_003482965.1_ASM348296v1_genomic.fna.gz]
[2023-06-17 18:03:46,090] [INFO] Query marker FASTA was written to GCA_003482965.1_ASM348296v1_genomic.fna/markers.fasta
[2023-06-17 18:03:46,091] [INFO] Task started: Blastn
[2023-06-17 18:03:46,091] [INFO] Running command: blastn -query GCA_003482965.1_ASM348296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/reference_markers.fasta -out GCA_003482965.1_ASM348296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:03:46,675] [INFO] Task succeeded: Blastn
[2023-06-17 18:03:46,678] [INFO] Selected 26 target genomes.
[2023-06-17 18:03:46,678] [INFO] Target genome list was writen to GCA_003482965.1_ASM348296v1_genomic.fna/target_genomes.txt
[2023-06-17 18:03:46,679] [INFO] Task started: fastANI
[2023-06-17 18:03:46,679] [INFO] Running command: fastANI --query /var/lib/cwl/stga88d78a6-c1d5-4203-9fac-46a9f0348db5/GCA_003482965.1_ASM348296v1_genomic.fna.gz --refList GCA_003482965.1_ASM348296v1_genomic.fna/target_genomes.txt --output GCA_003482965.1_ASM348296v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:04:01,422] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:01,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:04:01,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:04:01,439] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 18:04:01,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 18:04:01,439] [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
Croceibacter atlanticus	strain=HTCC2559	GCA_000196315.1	313588	313588	type	True	98.582	510	543	95	conclusive
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.208	75	543	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.208	75	543	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	76.6253	54	543	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	76.3894	50	543	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.3668	78	543	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.3644	80	543	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1897	52	543	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.1635	66	543	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	76.1453	52	543	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.1221	63	543	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.1135	53	543	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.0892	63	543	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.0851	65	543	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	75.9624	61	543	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	75.9309	63	543	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.8826	71	543	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	75.8662	66	543	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	75.8659	65	543	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	75.6452	56	543	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:04:01,442] [INFO] DFAST Taxonomy check result was written to GCA_003482965.1_ASM348296v1_genomic.fna/tc_result.tsv
[2023-06-17 18:04:01,442] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:04:01,442] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:04:01,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/checkm_data
[2023-06-17 18:04:01,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:04:01,468] [INFO] Task started: CheckM
[2023-06-17 18:04:01,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003482965.1_ASM348296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003482965.1_ASM348296v1_genomic.fna/checkm_input GCA_003482965.1_ASM348296v1_genomic.fna/checkm_result
[2023-06-17 18:04:22,880] [INFO] Task succeeded: CheckM
[2023-06-17 18:04:22,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:04:22,898] [INFO] ===== Completeness check finished =====
[2023-06-17 18:04:22,898] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:04:22,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003482965.1_ASM348296v1_genomic.fna/markers.fasta)
[2023-06-17 18:04:22,899] [INFO] Task started: Blastn
[2023-06-17 18:04:22,899] [INFO] Running command: blastn -query GCA_003482965.1_ASM348296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a8529b-8e59-49b4-a541-d29053be5823/dqc_reference/reference_markers_gtdb.fasta -out GCA_003482965.1_ASM348296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:04:23,720] [INFO] Task succeeded: Blastn
[2023-06-17 18:04:23,724] [INFO] Selected 26 target genomes.
[2023-06-17 18:04:23,724] [INFO] Target genome list was writen to GCA_003482965.1_ASM348296v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:04:23,738] [INFO] Task started: fastANI
[2023-06-17 18:04:23,738] [INFO] Running command: fastANI --query /var/lib/cwl/stga88d78a6-c1d5-4203-9fac-46a9f0348db5/GCA_003482965.1_ASM348296v1_genomic.fna.gz --refList GCA_003482965.1_ASM348296v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003482965.1_ASM348296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:04:38,066] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:38,083] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:04:38,083] [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_000196315.1	s__Croceibacter atlanticus	98.582	510	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceibacter	95.0	98.48	98.33	0.94	0.89	6	conclusive
GCF_014297365.1	s__Winogradskyella echinorum	77.208	75	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014764305.1	s__Mesoflavibacter profundi	76.9035	69	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.8068	60	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	76.6248	54	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.5414	53	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	76.4417	70	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.4385	66	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.4349	76	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	76.4327	61	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	76.4101	96	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	76.3894	50	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.3668	78	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	76.3012	61	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.1897	52	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.1668	79	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.1453	52	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.0892	63	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869935.1	s__Winogradskyella algicola	76.0851	65	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.0772	76	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.0442	60	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	75.8826	71	543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-17 18:04:38,085] [INFO] GTDB search result was written to GCA_003482965.1_ASM348296v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:04:38,086] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:04:38,090] [INFO] DFAST_QC result json was written to GCA_003482965.1_ASM348296v1_genomic.fna/dqc_result.json
[2023-06-17 18:04:38,091] [INFO] DFAST_QC completed!
[2023-06-17 18:04:38,091] [INFO] Total running time: 0h0m59s