[2024-01-24 13:57:13,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference
[2024-01-24 13:57:14,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,665] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg22a7ae06-b10c-4fd7-ab1b-5b5c3c587611/GCF_001047675.1_ASM104767v1_genomic.fna.gz | prodigal -d GCF_001047675.1_ASM104767v1_genomic.fna/cds.fna -a GCF_001047675.1_ASM104767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:25,622] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:25,623] [INFO] Task started: HMMsearch
[2024-01-24 13:57:25,623] [INFO] Running command: hmmsearch --tblout GCF_001047675.1_ASM104767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/reference_markers.hmm GCF_001047675.1_ASM104767v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:25,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:25,904] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg22a7ae06-b10c-4fd7-ab1b-5b5c3c587611/GCF_001047675.1_ASM104767v1_genomic.fna.gz]
[2024-01-24 13:57:25,938] [INFO] Query marker FASTA was written to GCF_001047675.1_ASM104767v1_genomic.fna/markers.fasta
[2024-01-24 13:57:25,939] [INFO] Task started: Blastn
[2024-01-24 13:57:25,939] [INFO] Running command: blastn -query GCF_001047675.1_ASM104767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/reference_markers.fasta -out GCF_001047675.1_ASM104767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:26,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:26,733] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:26,734] [INFO] Target genome list was writen to GCF_001047675.1_ASM104767v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:26,738] [INFO] Task started: fastANI
[2024-01-24 13:57:26,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a7ae06-b10c-4fd7-ab1b-5b5c3c587611/GCF_001047675.1_ASM104767v1_genomic.fna.gz --refList GCF_001047675.1_ASM104767v1_genomic.fna/target_genomes.txt --output GCF_001047675.1_ASM104767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:36,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:36,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:36,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:36,992] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:36,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:36,992] [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
Yersinia aleksiciae	strain=159	GCA_001047675.1	263819	263819	type	True	100.0	1332	1333	95	conclusive
Yersinia bercovieri	strain=ATCC 43970	GCA_013282745.1	634	634	type	True	91.3141	1096	1333	95	below_threshold
Yersinia bercovieri	strain=ATCC 43970	GCA_000167975.1	634	634	type	True	91.2735	1027	1333	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_013282725.1	33060	33060	type	True	90.268	1087	1333	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_000167995.1	33060	33060	type	True	90.0786	1041	1333	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	84.2127	893	1333	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.6487	413	1333	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.058	398	1333	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.9561	386	1333	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.9262	365	1333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:36,994] [INFO] DFAST Taxonomy check result was written to GCF_001047675.1_ASM104767v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:36,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:36,995] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:36,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/checkm_data
[2024-01-24 13:57:36,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:37,043] [INFO] Task started: CheckM
[2024-01-24 13:57:37,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001047675.1_ASM104767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001047675.1_ASM104767v1_genomic.fna/checkm_input GCF_001047675.1_ASM104767v1_genomic.fna/checkm_result
[2024-01-24 13:58:16,920] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:16,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:16,942] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:16,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:16,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001047675.1_ASM104767v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:16,943] [INFO] Task started: Blastn
[2024-01-24 13:58:16,944] [INFO] Running command: blastn -query GCF_001047675.1_ASM104767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c4be10-451d-40ce-8943-a4fcaffb6d19/dqc_reference/reference_markers_gtdb.fasta -out GCF_001047675.1_ASM104767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,047] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:18,047] [INFO] Target genome list was writen to GCF_001047675.1_ASM104767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:18,056] [INFO] Task started: fastANI
[2024-01-24 13:58:18,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a7ae06-b10c-4fd7-ab1b-5b5c3c587611/GCF_001047675.1_ASM104767v1_genomic.fna.gz --refList GCF_001047675.1_ASM104767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001047675.1_ASM104767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:33,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:33,577] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:33,578] [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_001047675.1	s__Yersinia aleksiciae	100.0	1332	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	conclusive
GCF_013282745.1	s__Yersinia bercovieri	91.3141	1096	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	-
GCF_013282725.1	s__Yersinia mollaretii	90.2662	1088	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	-
GCF_000312485.1	s__Yersinia massiliensis	85.9591	1043	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.58	95.54	0.91	0.88	22	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.3204	1024	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001152565.1	s__Yersinia pekkanenii	85.3183	967	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_003600645.1	s__Yersinia rochesterensis	85.1083	996	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_900460525.1	s__Yersinia kristensenii	84.9954	978	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_902726525.1	s__Yersinia enterocolitica_H	84.9883	972	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_000754805.1	s__Yersinia frederiksenii	84.9669	1031	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_001995075.1	s__Yersinia enterocolitica_F	84.8509	1005	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001155565.1	s__Yersinia frederiksenii_A	84.4613	1011	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	-
GCF_002951615.1	s__Rahnella sp002951615	79.3031	373	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834385.1	s__Rahnella sp002834385	79.0605	357	1333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,579] [INFO] GTDB search result was written to GCF_001047675.1_ASM104767v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:33,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:33,584] [INFO] DFAST_QC result json was written to GCF_001047675.1_ASM104767v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:33,584] [INFO] DFAST_QC completed!
[2024-01-24 13:58:33,584] [INFO] Total running time: 0h1m20s