[2024-01-24 11:26:12,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,160] [INFO] DQC Reference Directory: /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference
[2024-01-24 11:26:13,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,559] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgb15803d8-9bc4-4b5c-8738-910efeaeb6f1/GCF_007990795.1_ASM799079v1_genomic.fna.gz | prodigal -d GCF_007990795.1_ASM799079v1_genomic.fna/cds.fna -a GCF_007990795.1_ASM799079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:27,107] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:27,107] [INFO] Task started: HMMsearch
[2024-01-24 11:26:27,107] [INFO] Running command: hmmsearch --tblout GCF_007990795.1_ASM799079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/reference_markers.hmm GCF_007990795.1_ASM799079v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:27,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:27,423] [INFO] Found 6/6 markers.
[2024-01-24 11:26:27,455] [INFO] Query marker FASTA was written to GCF_007990795.1_ASM799079v1_genomic.fna/markers.fasta
[2024-01-24 11:26:27,455] [INFO] Task started: Blastn
[2024-01-24 11:26:27,455] [INFO] Running command: blastn -query GCF_007990795.1_ASM799079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/reference_markers.fasta -out GCF_007990795.1_ASM799079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:28,152] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:28,155] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:28,155] [INFO] Target genome list was writen to GCF_007990795.1_ASM799079v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:28,159] [INFO] Task started: fastANI
[2024-01-24 11:26:28,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgb15803d8-9bc4-4b5c-8738-910efeaeb6f1/GCF_007990795.1_ASM799079v1_genomic.fna.gz --refList GCF_007990795.1_ASM799079v1_genomic.fna/target_genomes.txt --output GCF_007990795.1_ASM799079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:35,502] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:35,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:35,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:35,511] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:35,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:35,512] [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
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	100.0	1240	1244	95	conclusive
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	99.9994	1213	1244	95	conclusive
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	84.8417	849	1244	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	80.7812	569	1244	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	80.7375	570	1244	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	79.3891	371	1244	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	79.1277	387	1244	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.1046	62	1244	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.8944	61	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:35,514] [INFO] DFAST Taxonomy check result was written to GCF_007990795.1_ASM799079v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:35,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:35,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:35,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/checkm_data
[2024-01-24 11:26:35,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:35,559] [INFO] Task started: CheckM
[2024-01-24 11:26:35,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990795.1_ASM799079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990795.1_ASM799079v1_genomic.fna/checkm_input GCF_007990795.1_ASM799079v1_genomic.fna/checkm_result
[2024-01-24 11:27:19,699] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:19,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:19,724] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:19,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:19,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990795.1_ASM799079v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:19,725] [INFO] Task started: Blastn
[2024-01-24 11:27:19,725] [INFO] Running command: blastn -query GCF_007990795.1_ASM799079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9d22574-dea3-496f-b522-e7870d66052f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990795.1_ASM799079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:20,627] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:20,630] [INFO] Selected 7 target genomes.
[2024-01-24 11:27:20,631] [INFO] Target genome list was writen to GCF_007990795.1_ASM799079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:20,636] [INFO] Task started: fastANI
[2024-01-24 11:27:20,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgb15803d8-9bc4-4b5c-8738-910efeaeb6f1/GCF_007990795.1_ASM799079v1_genomic.fna.gz --refList GCF_007990795.1_ASM799079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990795.1_ASM799079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:26,122] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:26,129] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:26,129] [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_000382425.1	s__Empedobacter brevis	99.9994	1213	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	conclusive
GCF_004785645.1	s__Empedobacter tilapiae	84.8327	850	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378465.1	s__Empedobacter sp002378465	84.7264	751	1244	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	84.6647	818	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCF_013116755.1	s__Empedobacter stercoris	83.7748	677	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_900115015.1	s__Algoriella xinjiangensis	81.5719	664	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCF_900142565.1	s__Chishuiella changwenlii	80.748	569	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,131] [INFO] GTDB search result was written to GCF_007990795.1_ASM799079v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:26,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:26,134] [INFO] DFAST_QC result json was written to GCF_007990795.1_ASM799079v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:26,134] [INFO] DFAST_QC completed!
[2024-01-24 11:27:26,134] [INFO] Total running time: 0h1m14s