[2024-01-24 13:31:12,054] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,056] [INFO] DQC Reference Directory: /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference
[2024-01-24 13:31:13,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,275] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb9ce8a1-8679-4152-a996-254acee2d2aa/GCF_004369705.1_ASM436970v1_genomic.fna.gz | prodigal -d GCF_004369705.1_ASM436970v1_genomic.fna/cds.fna -a GCF_004369705.1_ASM436970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:34,563] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:34,563] [INFO] Task started: HMMsearch
[2024-01-24 13:31:34,563] [INFO] Running command: hmmsearch --tblout GCF_004369705.1_ASM436970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/reference_markers.hmm GCF_004369705.1_ASM436970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:34,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:34,808] [INFO] Found 6/6 markers.
[2024-01-24 13:31:34,859] [INFO] Query marker FASTA was written to GCF_004369705.1_ASM436970v1_genomic.fna/markers.fasta
[2024-01-24 13:31:34,859] [INFO] Task started: Blastn
[2024-01-24 13:31:34,859] [INFO] Running command: blastn -query GCF_004369705.1_ASM436970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/reference_markers.fasta -out GCF_004369705.1_ASM436970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:35,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:35,543] [INFO] Selected 20 target genomes.
[2024-01-24 13:31:35,543] [INFO] Target genome list was writen to GCF_004369705.1_ASM436970v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:35,552] [INFO] Task started: fastANI
[2024-01-24 13:31:35,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb9ce8a1-8679-4152-a996-254acee2d2aa/GCF_004369705.1_ASM436970v1_genomic.fna.gz --refList GCF_004369705.1_ASM436970v1_genomic.fna/target_genomes.txt --output GCF_004369705.1_ASM436970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,407] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:58,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,407] [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 circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	100.0	1907	1908	95	conclusive
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	99.9959	1892	1908	95	conclusive
Flavobacterium cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	89.8829	1483	1908	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.9774	1135	1908	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.9481	1116	1908	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	82.7977	1060	1908	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.7689	1032	1908	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.7481	1061	1908	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	82.7235	1063	1908	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	82.6857	1005	1908	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	82.3134	951	1908	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	82.216	947	1908	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	82.0273	1014	1908	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.8481	1009	1908	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	81.697	959	1908	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	81.0721	846	1908	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	80.9484	894	1908	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	80.8344	954	1908	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.7574	935	1908	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.7872	127	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,412] [INFO] DFAST Taxonomy check result was written to GCF_004369705.1_ASM436970v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/checkm_data
[2024-01-24 13:31:58,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,481] [INFO] Task started: CheckM
[2024-01-24 13:31:58,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004369705.1_ASM436970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004369705.1_ASM436970v1_genomic.fna/checkm_input GCF_004369705.1_ASM436970v1_genomic.fna/checkm_result
[2024-01-24 13:33:02,015] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:02,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,044] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:02,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:02,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004369705.1_ASM436970v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:02,045] [INFO] Task started: Blastn
[2024-01-24 13:33:02,045] [INFO] Running command: blastn -query GCF_004369705.1_ASM436970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7c90619-d7b9-4a69-8b3a-42d58287a129/dqc_reference/reference_markers_gtdb.fasta -out GCF_004369705.1_ASM436970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:03,058] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:03,062] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:03,062] [INFO] Target genome list was writen to GCF_004369705.1_ASM436970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:03,076] [INFO] Task started: fastANI
[2024-01-24 13:33:03,076] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb9ce8a1-8679-4152-a996-254acee2d2aa/GCF_004369705.1_ASM436970v1_genomic.fna.gz --refList GCF_004369705.1_ASM436970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004369705.1_ASM436970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:25,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:25,931] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:25,931] [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_004345565.1	s__Flavobacterium circumlabens	99.9959	1892	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	conclusive
GCF_009674775.1	s__Flavobacterium sp009674775	89.9772	1437	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003996965.1	s__Flavobacterium cupreum	89.8623	1485	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105115.1	s__Flavobacterium sp003105115	83.1057	1039	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	83.0586	1124	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011751075.1	s__Flavobacterium sp011751075	83.0148	1009	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	83.0033	1099	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900107365.1	s__Flavobacterium aquidurense	82.8334	997	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001404985.1	s__Flavobacterium aquidurense_B	82.8025	1064	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844035.1	s__Flavobacterium sp014844035	82.7644	1090	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686925.1	s__Flavobacterium piscis	82.74	1062	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_001422725.1	s__Flavobacterium sp001422725	82.7038	1094	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900129595.1	s__Flavobacterium frigidimaris	82.6847	1025	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.6049	1137	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711165.2	s__Flavobacterium sp009711165	82.4116	1072	1908	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	81.7156	983	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789235.1	s__Flavobacterium sp009789235	81.7119	957	1908	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 13:33:25,933] [INFO] GTDB search result was written to GCF_004369705.1_ASM436970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:25,933] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:25,938] [INFO] DFAST_QC result json was written to GCF_004369705.1_ASM436970v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:25,938] [INFO] DFAST_QC completed!
[2024-01-24 13:33:25,938] [INFO] Total running time: 0h2m14s