[2024-01-24 12:45:20,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference
[2024-01-24 12:45:21,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,818] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg72a5a48e-752c-4c33-9b75-4bdd6f3d0016/GCF_017948675.1_ASM1794867v1_genomic.fna.gz | prodigal -d GCF_017948675.1_ASM1794867v1_genomic.fna/cds.fna -a GCF_017948675.1_ASM1794867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:33,499] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:33,500] [INFO] Task started: HMMsearch
[2024-01-24 12:45:33,500] [INFO] Running command: hmmsearch --tblout GCF_017948675.1_ASM1794867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/reference_markers.hmm GCF_017948675.1_ASM1794867v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:33,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:33,754] [INFO] Found 6/6 markers.
[2024-01-24 12:45:33,787] [INFO] Query marker FASTA was written to GCF_017948675.1_ASM1794867v1_genomic.fna/markers.fasta
[2024-01-24 12:45:33,787] [INFO] Task started: Blastn
[2024-01-24 12:45:33,787] [INFO] Running command: blastn -query GCF_017948675.1_ASM1794867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/reference_markers.fasta -out GCF_017948675.1_ASM1794867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:34,486] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:34,492] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:34,492] [INFO] Target genome list was writen to GCF_017948675.1_ASM1794867v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:34,508] [INFO] Task started: fastANI
[2024-01-24 12:45:34,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a5a48e-752c-4c33-9b75-4bdd6f3d0016/GCF_017948675.1_ASM1794867v1_genomic.fna.gz --refList GCF_017948675.1_ASM1794867v1_genomic.fna/target_genomes.txt --output GCF_017948675.1_ASM1794867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:50,192] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:50,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:50,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:50,208] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:50,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:50,208] [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 flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	100.0	1192	1195	95	conclusive
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	82.5901	743	1195	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	80.8412	625	1195	95	below_threshold
Flavobacterium segetis	strain=DSM 19741	GCA_900129575.1	271157	271157	type	True	80.679	639	1195	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	80.6245	625	1195	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	80.5924	627	1195	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	80.5817	618	1195	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.4202	622	1195	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	80.1017	543	1195	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	80.0896	539	1195	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	80.0249	559	1195	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	79.5121	493	1195	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	79.3493	436	1195	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.8549	416	1195	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	78.7168	423	1195	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.5927	368	1195	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.5687	345	1195	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3682	389	1195	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	78.3173	307	1195	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.2012	75	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:50,210] [INFO] DFAST Taxonomy check result was written to GCF_017948675.1_ASM1794867v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:50,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:50,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:50,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/checkm_data
[2024-01-24 12:45:50,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:50,247] [INFO] Task started: CheckM
[2024-01-24 12:45:50,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017948675.1_ASM1794867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017948675.1_ASM1794867v1_genomic.fna/checkm_input GCF_017948675.1_ASM1794867v1_genomic.fna/checkm_result
[2024-01-24 12:46:27,283] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:27,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:27,311] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:27,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:27,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017948675.1_ASM1794867v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:27,312] [INFO] Task started: Blastn
[2024-01-24 12:46:27,312] [INFO] Running command: blastn -query GCF_017948675.1_ASM1794867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda08df8c-abe0-4c8d-93e2-f3f78ffe29fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_017948675.1_ASM1794867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:28,258] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:28,262] [INFO] Selected 18 target genomes.
[2024-01-24 12:46:28,262] [INFO] Target genome list was writen to GCF_017948675.1_ASM1794867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:28,310] [INFO] Task started: fastANI
[2024-01-24 12:46:28,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a5a48e-752c-4c33-9b75-4bdd6f3d0016/GCF_017948675.1_ASM1794867v1_genomic.fna.gz --refList GCF_017948675.1_ASM1794867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017948675.1_ASM1794867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:41,428] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:41,449] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:41,449] [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_014281985.1	s__Flavobacterium sp014281985	98.0482	1070	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	conclusive
GCF_003688495.1	s__Flavobacterium weaverense	82.5903	743	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143245.1	s__Flavobacterium fryxellicola	80.8284	625	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129575.1	s__Flavobacterium segetis	80.6542	640	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	80.6325	622	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349135.1	s__Flavobacterium sandaracinum	80.6069	624	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142695.1	s__Flavobacterium xanthum	80.6016	615	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCF_002754315.1	s__Flavobacterium sp002754315	80.5697	614	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCA_017995345.1	s__Flavobacterium sp017995345	80.5286	525	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_000812945.1	s__Flavobacterium sp000812945	80.4884	538	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	80.4509	617	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_017875765.1	s__Flavobacterium sp017875765	80.4007	557	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_000744835.1	s__Flavobacterium sp000744835	80.1628	549	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	80.0949	538	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_900108015.1	s__Flavobacterium urumqiense	80.0706	545	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	80.0219	560	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	79.5209	491	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_000813005.1	s__Flavobacterium sp000813005	78.9729	456	1195	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.28	97.24	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:41,452] [INFO] GTDB search result was written to GCF_017948675.1_ASM1794867v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:41,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:41,457] [INFO] DFAST_QC result json was written to GCF_017948675.1_ASM1794867v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:41,457] [INFO] DFAST_QC completed!
[2024-01-24 12:46:41,457] [INFO] Total running time: 0h1m21s