[2024-01-24 12:31:18,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:18,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:18,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference
[2024-01-24 12:31:20,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:20,109] [INFO] Task started: Prodigal
[2024-01-24 12:31:20,109] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd9f1ce2-b1c1-4d26-8257-c11e90018f42/GCF_027111295.1_ASM2711129v2_genomic.fna.gz | prodigal -d GCF_027111295.1_ASM2711129v2_genomic.fna/cds.fna -a GCF_027111295.1_ASM2711129v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,565] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,565] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,566] [INFO] Running command: hmmsearch --tblout GCF_027111295.1_ASM2711129v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/reference_markers.hmm GCF_027111295.1_ASM2711129v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,833] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,876] [INFO] Query marker FASTA was written to GCF_027111295.1_ASM2711129v2_genomic.fna/markers.fasta
[2024-01-24 12:31:36,876] [INFO] Task started: Blastn
[2024-01-24 12:31:36,876] [INFO] Running command: blastn -query GCF_027111295.1_ASM2711129v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/reference_markers.fasta -out GCF_027111295.1_ASM2711129v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,510] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:37,510] [INFO] Target genome list was writen to GCF_027111295.1_ASM2711129v2_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,520] [INFO] Task started: fastANI
[2024-01-24 12:31:37,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd9f1ce2-b1c1-4d26-8257-c11e90018f42/GCF_027111295.1_ASM2711129v2_genomic.fna.gz --refList GCF_027111295.1_ASM2711129v2_genomic.fna/target_genomes.txt --output GCF_027111295.1_ASM2711129v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:01,401] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:01,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:01,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:01,416] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:01,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:01,416] [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 endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	84.8463	1266	1944	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	84.32	1275	1944	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	84.3171	1268	1944	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	84.2453	1262	1944	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	83.7811	1120	1944	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.7624	1159	1944	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.5028	1187	1944	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	83.2408	1151	1944	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.0642	1148	1944	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	83.0265	1054	1944	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	83.0235	1083	1944	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	83.007	1095	1944	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	82.9964	1038	1944	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	82.9454	1091	1944	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	82.8514	1019	1944	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	82.8133	1000	1944	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	82.7597	1035	1944	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	82.7132	1146	1944	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	82.5383	952	1944	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	82.3211	1095	1944	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.7912	206	1944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,417] [INFO] DFAST Taxonomy check result was written to GCF_027111295.1_ASM2711129v2_genomic.fna/tc_result.tsv
[2024-01-24 12:32:01,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:01,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:01,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/checkm_data
[2024-01-24 12:32:01,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:01,475] [INFO] Task started: CheckM
[2024-01-24 12:32:01,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027111295.1_ASM2711129v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027111295.1_ASM2711129v2_genomic.fna/checkm_input GCF_027111295.1_ASM2711129v2_genomic.fna/checkm_result
[2024-01-24 12:32:48,720] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:48,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:48,738] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:48,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:48,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027111295.1_ASM2711129v2_genomic.fna/markers.fasta)
[2024-01-24 12:32:48,738] [INFO] Task started: Blastn
[2024-01-24 12:32:48,738] [INFO] Running command: blastn -query GCF_027111295.1_ASM2711129v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ea1bbb-23cd-4a8b-a1a8-823cae70f060/dqc_reference/reference_markers_gtdb.fasta -out GCF_027111295.1_ASM2711129v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:49,671] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:49,674] [INFO] Selected 25 target genomes.
[2024-01-24 12:32:49,674] [INFO] Target genome list was writen to GCF_027111295.1_ASM2711129v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:49,699] [INFO] Task started: fastANI
[2024-01-24 12:32:49,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd9f1ce2-b1c1-4d26-8257-c11e90018f42/GCF_027111295.1_ASM2711129v2_genomic.fna.gz --refList GCF_027111295.1_ASM2711129v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027111295.1_ASM2711129v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:17,942] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:17,956] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:17,957] [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_017352115.1	s__Flavobacterium sp017352115	84.8652	1265	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	84.3305	1274	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_001428525.1	s__Flavobacterium sp001428525	83.8752	1209	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129795.1	s__Flavobacterium sp900129795	83.8096	1210	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900129555.1	s__Flavobacterium defluvii	83.7786	1120	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	83.7233	1179	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	83.6266	1220	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_001429765.1	s__Flavobacterium sp001429765	83.4528	1153	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.97	0.97	2	-
GCA_017744675.1	s__Flavobacterium sp017744675	83.2993	1100	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	83.2224	1154	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	83.0263	1054	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	82.9993	1096	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003312915.1	s__Flavobacterium sp003312915	82.9714	1089	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	82.9332	1056	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	82.9084	1146	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	82.8512	1018	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425445.1	s__Flavobacterium denitrificans	82.824	998	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	82.7837	1121	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004352915.1	s__Flavobacterium zhairuonense	82.7678	1034	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101855.1	s__Flavobacterium anhuiense	82.7649	1111	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	-
GCF_001429295.1	s__Flavobacterium sp001429295	82.725	1093	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_900112575.1	s__Flavobacterium phragmitis	82.6914	1149	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711135.1	s__Flavobacterium sp009711135	82.6821	1006	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007341385.1	s__Flavobacterium daemonense	82.5508	950	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634245.1	s__Flavobacterium foetidum	82.3266	1094	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:17,958] [INFO] GTDB search result was written to GCF_027111295.1_ASM2711129v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:17,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:17,963] [INFO] DFAST_QC result json was written to GCF_027111295.1_ASM2711129v2_genomic.fna/dqc_result.json
[2024-01-24 12:33:17,964] [INFO] DFAST_QC completed!
[2024-01-24 12:33:17,964] [INFO] Total running time: 0h1m59s