[2024-01-24 13:39:59,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:39:59,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:39:59,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference
[2024-01-24 13:40:00,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:00,816] [INFO] Task started: Prodigal
[2024-01-24 13:40:00,816] [INFO] Running command: gunzip -c /var/lib/cwl/stgcabcf3d8-db7b-4111-81da-d281ca82bc62/GCF_030409845.1_ASM3040984v1_genomic.fna.gz | prodigal -d GCF_030409845.1_ASM3040984v1_genomic.fna/cds.fna -a GCF_030409845.1_ASM3040984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:16,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:16,639] [INFO] Task started: HMMsearch
[2024-01-24 13:40:16,639] [INFO] Running command: hmmsearch --tblout GCF_030409845.1_ASM3040984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/reference_markers.hmm GCF_030409845.1_ASM3040984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:16,937] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:16,938] [INFO] Found 6/6 markers.
[2024-01-24 13:40:16,978] [INFO] Query marker FASTA was written to GCF_030409845.1_ASM3040984v1_genomic.fna/markers.fasta
[2024-01-24 13:40:16,978] [INFO] Task started: Blastn
[2024-01-24 13:40:16,978] [INFO] Running command: blastn -query GCF_030409845.1_ASM3040984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/reference_markers.fasta -out GCF_030409845.1_ASM3040984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:17,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:17,692] [INFO] Selected 24 target genomes.
[2024-01-24 13:40:17,693] [INFO] Target genome list was writen to GCF_030409845.1_ASM3040984v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:17,700] [INFO] Task started: fastANI
[2024-01-24 13:40:17,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgcabcf3d8-db7b-4111-81da-d281ca82bc62/GCF_030409845.1_ASM3040984v1_genomic.fna.gz --refList GCF_030409845.1_ASM3040984v1_genomic.fna/target_genomes.txt --output GCF_030409845.1_ASM3040984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:41,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:41,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:41,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:41,673] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:41,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:41,673] [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 hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	84.4989	1065	1665	95	below_threshold
Flavobacterium hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	84.4759	1089	1665	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	80.1356	741	1665	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	80.1038	666	1665	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	80.0126	778	1665	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	79.9764	639	1665	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	79.9688	588	1665	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	79.9633	711	1665	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	79.9391	720	1665	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	79.9317	676	1665	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	79.9059	716	1665	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	79.9033	703	1665	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	79.8864	716	1665	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	79.8444	647	1665	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	79.8123	708	1665	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	79.6822	621	1665	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	79.6051	599	1665	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	79.5848	657	1665	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	79.5607	662	1665	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	79.5558	627	1665	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	79.4959	663	1665	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	79.4347	536	1665	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	79.0428	543	1665	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.4027	250	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:41,675] [INFO] DFAST Taxonomy check result was written to GCF_030409845.1_ASM3040984v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:41,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:41,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:41,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/checkm_data
[2024-01-24 13:40:41,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:41,745] [INFO] Task started: CheckM
[2024-01-24 13:40:41,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409845.1_ASM3040984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409845.1_ASM3040984v1_genomic.fna/checkm_input GCF_030409845.1_ASM3040984v1_genomic.fna/checkm_result
[2024-01-24 13:41:31,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409845.1_ASM3040984v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,318] [INFO] Task started: Blastn
[2024-01-24 13:41:31,318] [INFO] Running command: blastn -query GCF_030409845.1_ASM3040984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763758b7-878e-4417-9d56-bd93a022424f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409845.1_ASM3040984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,295] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:32,295] [INFO] Target genome list was writen to GCF_030409845.1_ASM3040984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,303] [INFO] Task started: fastANI
[2024-01-24 13:41:32,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgcabcf3d8-db7b-4111-81da-d281ca82bc62/GCF_030409845.1_ASM3040984v1_genomic.fna.gz --refList GCF_030409845.1_ASM3040984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409845.1_ASM3040984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,787] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,797] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,797] [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_003668995.1	s__Flavobacterium sp003668995	88.2186	1206	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594725.1	s__Flavobacterium sp015594725	86.1673	1047	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813005.1	s__Flavobacterium sp000813005	84.8446	1091	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.28	97.24	0.92	0.92	3	-
GCF_000737695.1	s__Flavobacterium hydatis	84.4903	1065	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009711165.2	s__Flavobacterium sp009711165	80.1367	716	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	80.1361	734	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351595.1	s__Flavobacterium sp015351595	80.1258	671	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018380615.1	s__Flavobacterium psychroterrae	80.0261	776	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217285.1	s__Flavobacterium hercynium	79.971	640	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900107365.1	s__Flavobacterium aquidurense	79.9567	678	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001686925.1	s__Flavobacterium piscis	79.9134	715	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	79.622	645	1665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,799] [INFO] GTDB search result was written to GCF_030409845.1_ASM3040984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,807] [INFO] DFAST_QC result json was written to GCF_030409845.1_ASM3040984v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,808] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,808] [INFO] Total running time: 0h1m47s