[2024-01-24 11:19:53,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference
[2024-01-24 11:19:55,046] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,048] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b12d4dd-22c9-4ccb-b8e1-f867ed627e55/GCF_003385895.1_ASM338589v1_genomic.fna.gz | prodigal -d GCF_003385895.1_ASM338589v1_genomic.fna/cds.fna -a GCF_003385895.1_ASM338589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,332] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,333] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,333] [INFO] Running command: hmmsearch --tblout GCF_003385895.1_ASM338589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/reference_markers.hmm GCF_003385895.1_ASM338589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:12,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:12,633] [INFO] Found 6/6 markers.
[2024-01-24 11:20:12,918] [INFO] Query marker FASTA was written to GCF_003385895.1_ASM338589v1_genomic.fna/markers.fasta
[2024-01-24 11:20:12,919] [INFO] Task started: Blastn
[2024-01-24 11:20:12,919] [INFO] Running command: blastn -query GCF_003385895.1_ASM338589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/reference_markers.fasta -out GCF_003385895.1_ASM338589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:13,623] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:13,627] [INFO] Selected 21 target genomes.
[2024-01-24 11:20:13,628] [INFO] Target genome list was writen to GCF_003385895.1_ASM338589v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:13,636] [INFO] Task started: fastANI
[2024-01-24 11:20:13,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b12d4dd-22c9-4ccb-b8e1-f867ed627e55/GCF_003385895.1_ASM338589v1_genomic.fna.gz --refList GCF_003385895.1_ASM338589v1_genomic.fna/target_genomes.txt --output GCF_003385895.1_ASM338589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:37,643] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:37,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:37,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:37,666] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:37,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:37,667] [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 cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	100.0	1625	1626	95	conclusive
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	85.9012	1141	1626	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	85.8039	1146	1626	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	85.3556	1152	1626	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	85.3465	1093	1626	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	84.1752	1011	1626	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	84.1518	1069	1626	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.7064	1069	1626	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	83.7059	1045	1626	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	83.6975	1066	1626	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	83.638	1031	1626	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.4736	1050	1626	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	83.4247	1056	1626	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.1499	1006	1626	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.1472	1035	1626	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.1452	1047	1626	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	82.8531	1056	1626	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	82.7638	961	1626	95	below_threshold
Flavobacterium ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	82.3862	904	1626	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	82.3344	901	1626	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.8725	163	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:37,668] [INFO] DFAST Taxonomy check result was written to GCF_003385895.1_ASM338589v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:37,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:37,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:37,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/checkm_data
[2024-01-24 11:20:37,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:37,723] [INFO] Task started: CheckM
[2024-01-24 11:20:37,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385895.1_ASM338589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385895.1_ASM338589v1_genomic.fna/checkm_input GCF_003385895.1_ASM338589v1_genomic.fna/checkm_result
[2024-01-24 11:21:29,206] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:29,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:29,230] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:29,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:29,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385895.1_ASM338589v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:29,231] [INFO] Task started: Blastn
[2024-01-24 11:21:29,231] [INFO] Running command: blastn -query GCF_003385895.1_ASM338589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c8eb656-3f12-4502-b804-291a85b51c1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385895.1_ASM338589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:30,218] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:30,221] [INFO] Selected 19 target genomes.
[2024-01-24 11:21:30,221] [INFO] Target genome list was writen to GCF_003385895.1_ASM338589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:30,234] [INFO] Task started: fastANI
[2024-01-24 11:21:30,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b12d4dd-22c9-4ccb-b8e1-f867ed627e55/GCF_003385895.1_ASM338589v1_genomic.fna.gz --refList GCF_003385895.1_ASM338589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385895.1_ASM338589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:52,176] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:52,196] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:52,197] [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_003385895.1	s__Flavobacterium cutihirudinis	100.0	1626	1626	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_000745775.1	s__Flavobacterium sp000745775	85.9347	1134	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	85.8315	1143	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	85.7824	1158	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	85.5558	1124	1626	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	85.3576	1152	1626	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	85.3528	1092	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383905.1	s__Flavobacterium branchiicola	84.3782	1178	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210235.1	s__Flavobacterium sp002210235	84.1874	1077	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_013388355.1	s__Flavobacterium sp013388355	84.0349	813	1626	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	83.9166	1048	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004119495.1	s__Flavobacterium sp004119495	83.8928	1002	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	83.6315	1032	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_001879205.1	s__Flavobacterium johnsoniae_A	83.5693	1058	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217395.1	s__Flavobacterium plurextorum	83.4817	1034	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_003122385.1	s__Flavobacterium crocinum	83.425	1056	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002304005.1	s__Flavobacterium sp002304005	83.1702	1015	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602525.1	s__Flavobacterium chilense	83.1337	1049	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_002217435.1	s__Flavobacterium reichenbachii	82.7662	961	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:52,199] [INFO] GTDB search result was written to GCF_003385895.1_ASM338589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:52,199] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:52,203] [INFO] DFAST_QC result json was written to GCF_003385895.1_ASM338589v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:52,203] [INFO] DFAST_QC completed!
[2024-01-24 11:21:52,203] [INFO] Total running time: 0h1m59s