[2024-01-24 13:22:55,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference
[2024-01-24 13:22:56,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,758] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,758] [INFO] Running command: gunzip -c /var/lib/cwl/stge22a69ce-91cd-428b-aafe-d20f25692c40/GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/cds.fna -a GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:05,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:05,875] [INFO] Task started: HMMsearch
[2024-01-24 13:23:05,875] [INFO] Running command: hmmsearch --tblout GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/reference_markers.hmm GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:06,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:06,148] [INFO] Found 6/6 markers.
[2024-01-24 13:23:06,177] [INFO] Query marker FASTA was written to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:23:06,178] [INFO] Task started: Blastn
[2024-01-24 13:23:06,178] [INFO] Running command: blastn -query GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/reference_markers.fasta -out GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:06,821] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:06,826] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:06,826] [INFO] Target genome list was writen to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:23:06,839] [INFO] Task started: fastANI
[2024-01-24 13:23:06,840] [INFO] Running command: fastANI --query /var/lib/cwl/stge22a69ce-91cd-428b-aafe-d20f25692c40/GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna.gz --refList GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:13,524] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:13,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:13,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:13,534] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:13,534] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:13,534] [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
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	100.0	1137	1137	95	conclusive
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	99.9822	1104	1137	95	conclusive
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	81.3152	599	1137	95	below_threshold
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	80.8518	584	1137	95	below_threshold
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	80.849	572	1137	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	79.8489	425	1137	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	79.5954	412	1137	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	79.2825	406	1137	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	75.8252	84	1137	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.3983	102	1137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,537] [INFO] DFAST Taxonomy check result was written to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:23:13,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:13,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:13,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/checkm_data
[2024-01-24 13:23:13,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:13,578] [INFO] Task started: CheckM
[2024-01-24 13:23:13,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/checkm_input GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:43,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:43,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:44,019] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:44,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:44,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:44,020] [INFO] Task started: Blastn
[2024-01-24 13:23:44,020] [INFO] Running command: blastn -query GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0275219f-8412-43cc-8133-6f693d297758/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:44,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:44,984] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:44,984] [INFO] Target genome list was writen to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:45,002] [INFO] Task started: fastANI
[2024-01-24 13:23:45,003] [INFO] Running command: fastANI --query /var/lib/cwl/stge22a69ce-91cd-428b-aafe-d20f25692c40/GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna.gz --refList GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:52,035] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:52,048] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:52,048] [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_900142565.1	s__Chishuiella changwenlii	100.0	1137	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_002378465.1	s__Empedobacter sp002378465	81.6027	593	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.64	95.90	0.90	0.86	24	-
GCF_013488205.1	s__Empedobacter falsenii_A	81.5398	632	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCA_002430925.1	s__Chishuiella sp002430925	81.3949	564	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785645.1	s__Empedobacter tilapiae	81.304	600	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013116755.1	s__Empedobacter stercoris	81.2791	533	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCA_002484335.1	s__Chishuiella sp002484335	81.1854	626	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115015.1	s__Algoriella xinjiangensis	81.1594	619	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCF_000382425.1	s__Empedobacter brevis	80.8585	583	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	-
GCA_003687725.1	s__Faecalibacter macacae	79.8867	423	1137	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:52,050] [INFO] GTDB search result was written to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:52,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:52,054] [INFO] DFAST_QC result json was written to GCF_900142565.1_IMG-taxon_2700988695_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:52,054] [INFO] DFAST_QC completed!
[2024-01-24 13:23:52,055] [INFO] Total running time: 0h0m57s