[2023-06-30 16:08:38,985] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:08:38,990] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:08:38,991] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference
[2023-06-30 16:08:40,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:08:40,202] [INFO] Task started: Prodigal
[2023-06-30 16:08:40,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c61195a-7a47-413d-bbda-e2cfa8033a53/GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna.gz | prodigal -d GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/cds.fna -a GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:08:50,067] [INFO] Task succeeded: Prodigal
[2023-06-30 16:08:50,067] [INFO] Task started: HMMsearch
[2023-06-30 16:08:50,067] [INFO] Running command: hmmsearch --tblout GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/reference_markers.hmm GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:08:50,267] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:08:50,268] [INFO] Found 6/6 markers.
[2023-06-30 16:08:50,292] [INFO] Query marker FASTA was written to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/markers.fasta
[2023-06-30 16:08:50,292] [INFO] Task started: Blastn
[2023-06-30 16:08:50,292] [INFO] Running command: blastn -query GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/reference_markers.fasta -out GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:08:50,982] [INFO] Task succeeded: Blastn
[2023-06-30 16:08:50,986] [INFO] Selected 28 target genomes.
[2023-06-30 16:08:50,987] [INFO] Target genome list was writen to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/target_genomes.txt
[2023-06-30 16:08:51,018] [INFO] Task started: fastANI
[2023-06-30 16:08:51,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c61195a-7a47-413d-bbda-e2cfa8033a53/GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna.gz --refList GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/target_genomes.txt --output GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:09:08,014] [INFO] Task succeeded: fastANI
[2023-06-30 16:09:08,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:09:08,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:09:08,036] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:09:08,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:09:08,037] [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
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	78.3283	377	787	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.2197	324	787	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.1867	318	787	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	78.0392	266	787	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	77.9939	316	787	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.9834	316	787	95	below_threshold
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	77.9749	231	787	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	77.77	252	787	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	77.7151	233	787	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	77.7098	243	787	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	77.7005	234	787	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	77.6835	220	787	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	77.6524	222	787	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	77.5599	225	787	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	77.5431	226	787	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	77.5275	222	787	95	below_threshold
Flavobacterium geliluteum	strain=P7388	GCA_017948595.1	2816120	2816120	type	True	77.2187	184	787	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	77.1936	197	787	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.1826	192	787	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.1098	175	787	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.0867	180	787	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	77.0752	253	787	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.004	190	787	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.002	185	787	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	76.9946	172	787	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.9755	214	787	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.9256	146	787	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	76.9248	173	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:09:08,039] [INFO] DFAST Taxonomy check result was written to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/tc_result.tsv
[2023-06-30 16:09:08,040] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:09:08,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:09:08,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/checkm_data
[2023-06-30 16:09:08,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:09:08,072] [INFO] Task started: CheckM
[2023-06-30 16:09:08,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/checkm_input GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/checkm_result
[2023-06-30 16:09:40,434] [INFO] Task succeeded: CheckM
[2023-06-30 16:09:40,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:09:40,455] [INFO] ===== Completeness check finished =====
[2023-06-30 16:09:40,455] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:09:40,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/markers.fasta)
[2023-06-30 16:09:40,456] [INFO] Task started: Blastn
[2023-06-30 16:09:40,456] [INFO] Running command: blastn -query GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8c0f1b5-806a-4483-ba55-afcfc8373bba/dqc_reference/reference_markers_gtdb.fasta -out GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:09:41,405] [INFO] Task succeeded: Blastn
[2023-06-30 16:09:41,409] [INFO] Selected 25 target genomes.
[2023-06-30 16:09:41,410] [INFO] Target genome list was writen to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:09:41,414] [INFO] Task started: fastANI
[2023-06-30 16:09:41,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c61195a-7a47-413d-bbda-e2cfa8033a53/GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna.gz --refList GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/target_genomes_gtdb.txt --output GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:09:55,845] [INFO] Task succeeded: fastANI
[2023-06-30 16:09:55,865] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:09:55,865] [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
GCA_903842575.1	s__Flavobacterium sp903842575	100.0	780	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004797125.1	s__Flavobacterium sangjuense	78.3283	377	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	78.2091	325	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	78.1982	317	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	78.1033	259	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	78.0259	267	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	77.9832	316	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCF_003634615.1	s__Flavobacterium sp002482945	77.9509	335	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.9446	329	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	77.9376	292	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	77.8018	266	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	77.7435	209	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	77.7392	233	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_014486695.1	s__Flavobacterium buctense	77.7279	307	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	77.7133	231	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	77.7024	149	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	77.7006	253	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	77.63	220	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693635.1	s__Flavobacterium sp009693635	77.5937	181	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	77.5545	190	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413745.1	s__Flavobacterium sp002413745	77.5484	242	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCA_017303755.1	s__Flavobacterium sp017303755	77.5394	272	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714905.1	s__Flavobacterium sp016714905	77.3196	211	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425425.1	s__Flavobacterium daejeonense	76.9248	173	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454195.1	s__Flavobacterium sp002454195	76.8863	134	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:09:55,867] [INFO] GTDB search result was written to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/result_gtdb.tsv
[2023-06-30 16:09:55,868] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:09:55,873] [INFO] DFAST_QC result json was written to GCA_903842575.1_freshwater_MAG_---_KTt_bin-1219_genomic.fna/dqc_result.json
[2023-06-30 16:09:55,874] [INFO] DFAST_QC completed!
[2023-06-30 16:09:55,874] [INFO] Total running time: 0h1m17s