[2024-01-24 13:45:45,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference
[2024-01-24 13:45:46,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:46,925] [INFO] Task started: Prodigal
[2024-01-24 13:45:46,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b786c52-d60f-47ee-891e-04596ddbc23f/GCF_003382565.3_ASM338256v3_genomic.fna.gz | prodigal -d GCF_003382565.3_ASM338256v3_genomic.fna/cds.fna -a GCF_003382565.3_ASM338256v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:58,977] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:58,978] [INFO] Task started: HMMsearch
[2024-01-24 13:45:58,978] [INFO] Running command: hmmsearch --tblout GCF_003382565.3_ASM338256v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/reference_markers.hmm GCF_003382565.3_ASM338256v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:59,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:59,300] [INFO] Found 6/6 markers.
[2024-01-24 13:45:59,347] [INFO] Query marker FASTA was written to GCF_003382565.3_ASM338256v3_genomic.fna/markers.fasta
[2024-01-24 13:45:59,348] [INFO] Task started: Blastn
[2024-01-24 13:45:59,348] [INFO] Running command: blastn -query GCF_003382565.3_ASM338256v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/reference_markers.fasta -out GCF_003382565.3_ASM338256v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:00,268] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:00,272] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:00,273] [INFO] Target genome list was writen to GCF_003382565.3_ASM338256v3_genomic.fna/target_genomes.txt
[2024-01-24 13:46:00,292] [INFO] Task started: fastANI
[2024-01-24 13:46:00,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b786c52-d60f-47ee-891e-04596ddbc23f/GCF_003382565.3_ASM338256v3_genomic.fna.gz --refList GCF_003382565.3_ASM338256v3_genomic.fna/target_genomes.txt --output GCF_003382565.3_ASM338256v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:18,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:18,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:18,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:18,145] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:18,145] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:18,145] [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
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	100.0	1485	1488	95	inconclusive
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	95.8381	1270	1488	95	inconclusive
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	94.5124	1192	1488	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	94.1168	1208	1488	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	94.1089	1215	1488	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	94.098	1216	1488	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	93.5233	1203	1488	95	below_threshold
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	93.4422	1178	1488	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	93.3008	1144	1488	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	93.2637	1181	1488	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.165	1205	1488	95	below_threshold
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	89.445	1124	1488	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6601	425	1488	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.5949	349	1488	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	78.3097	353	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:18,147] [INFO] DFAST Taxonomy check result was written to GCF_003382565.3_ASM338256v3_genomic.fna/tc_result.tsv
[2024-01-24 13:46:18,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:18,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:18,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/checkm_data
[2024-01-24 13:46:18,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:18,206] [INFO] Task started: CheckM
[2024-01-24 13:46:18,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003382565.3_ASM338256v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003382565.3_ASM338256v3_genomic.fna/checkm_input GCF_003382565.3_ASM338256v3_genomic.fna/checkm_result
[2024-01-24 13:46:58,735] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:58,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,761] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:58,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:58,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003382565.3_ASM338256v3_genomic.fna/markers.fasta)
[2024-01-24 13:46:58,762] [INFO] Task started: Blastn
[2024-01-24 13:46:58,763] [INFO] Running command: blastn -query GCF_003382565.3_ASM338256v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd27003f9-8cb9-45a6-a75c-15359e43f553/dqc_reference/reference_markers_gtdb.fasta -out GCF_003382565.3_ASM338256v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:00,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:00,029] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:00,029] [INFO] Target genome list was writen to GCF_003382565.3_ASM338256v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:00,045] [INFO] Task started: fastANI
[2024-01-24 13:47:00,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b786c52-d60f-47ee-891e-04596ddbc23f/GCF_003382565.3_ASM338256v3_genomic.fna.gz --refList GCF_003382565.3_ASM338256v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003382565.3_ASM338256v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:13,559] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:13,573] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:13,573] [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_003382565.2	s__Pectobacterium aquaticum	99.9437	1398	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	conclusive
GCF_900129615.1	s__Pectobacterium carotovorum	94.098	1216	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	93.6528	1237	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_002307355.1	s__Pectobacterium polaris	93.5219	1204	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_000754695.1	s__Pectobacterium brasiliense	93.2637	1181	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_000803315.1	s__Pectobacterium actinidiae	91.9581	1203	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_005497185.1	s__Pectobacterium polonicum	89.8913	1195	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019056595.1	s__Pectobacterium atrosepticum	89.5689	1188	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_002847345.1	s__Pectobacterium peruviense	89.5505	1188	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	-
GCF_000749845.1	s__Pectobacterium betavasculorum	89.264	1121	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:13,576] [INFO] GTDB search result was written to GCF_003382565.3_ASM338256v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:13,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:13,584] [INFO] DFAST_QC result json was written to GCF_003382565.3_ASM338256v3_genomic.fna/dqc_result.json
[2024-01-24 13:47:13,585] [INFO] DFAST_QC completed!
[2024-01-24 13:47:13,585] [INFO] Total running time: 0h1m28s