[2024-01-25 19:11:05,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference
[2024-01-25 19:11:07,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:07,008] [INFO] Task started: Prodigal
[2024-01-25 19:11:07,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b9469d1-b4c5-4374-8415-2a15a34b1e7f/GCF_900195285.2_Pc0421_3_genomic.fna.gz | prodigal -d GCF_900195285.2_Pc0421_3_genomic.fna/cds.fna -a GCF_900195285.2_Pc0421_3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:17,584] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:17,584] [INFO] Task started: HMMsearch
[2024-01-25 19:11:17,584] [INFO] Running command: hmmsearch --tblout GCF_900195285.2_Pc0421_3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/reference_markers.hmm GCF_900195285.2_Pc0421_3_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:17,829] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:17,830] [INFO] Found 6/6 markers.
[2024-01-25 19:11:17,866] [INFO] Query marker FASTA was written to GCF_900195285.2_Pc0421_3_genomic.fna/markers.fasta
[2024-01-25 19:11:17,867] [INFO] Task started: Blastn
[2024-01-25 19:11:17,867] [INFO] Running command: blastn -query GCF_900195285.2_Pc0421_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/reference_markers.fasta -out GCF_900195285.2_Pc0421_3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:18,717] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:18,719] [INFO] Selected 15 target genomes.
[2024-01-25 19:11:18,719] [INFO] Target genome list was writen to GCF_900195285.2_Pc0421_3_genomic.fna/target_genomes.txt
[2024-01-25 19:11:18,727] [INFO] Task started: fastANI
[2024-01-25 19:11:18,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9469d1-b4c5-4374-8415-2a15a34b1e7f/GCF_900195285.2_Pc0421_3_genomic.fna.gz --refList GCF_900195285.2_Pc0421_3_genomic.fna/target_genomes.txt --output GCF_900195285.2_Pc0421_3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:35,737] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:35,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:35,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:35,748] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:11:35,748] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:11:35,748] [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 parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	100.0	1530	1533	95	inconclusive
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	96.0184	1305	1533	95	inconclusive
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	93.8073	1263	1533	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	93.5126	1251	1533	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	93.4919	1281	1533	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	93.4655	1263	1533	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	93.457	1272	1533	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	93.4499	1278	1533	95	below_threshold
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	93.1427	1160	1533	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	93.1162	1160	1533	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.2383	1247	1533	95	below_threshold
Pectobacterium peruviense	strain=IFB5232	GCA_002847345.1	2066479	2066479	type	True	89.6776	1242	1533	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.6253	350	1533	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.4522	367	1533	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	78.3455	359	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:35,750] [INFO] DFAST Taxonomy check result was written to GCF_900195285.2_Pc0421_3_genomic.fna/tc_result.tsv
[2024-01-25 19:11:35,751] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:35,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:35,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/checkm_data
[2024-01-25 19:11:35,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:35,800] [INFO] Task started: CheckM
[2024-01-25 19:11:35,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900195285.2_Pc0421_3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900195285.2_Pc0421_3_genomic.fna/checkm_input GCF_900195285.2_Pc0421_3_genomic.fna/checkm_result
[2024-01-25 19:12:09,796] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:09,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:09,818] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:09,818] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:09,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900195285.2_Pc0421_3_genomic.fna/markers.fasta)
[2024-01-25 19:12:09,819] [INFO] Task started: Blastn
[2024-01-25 19:12:09,819] [INFO] Running command: blastn -query GCF_900195285.2_Pc0421_3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e53f780-1f49-4cca-a89d-f7326035eaa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900195285.2_Pc0421_3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:11,163] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:11,167] [INFO] Selected 8 target genomes.
[2024-01-25 19:12:11,167] [INFO] Target genome list was writen to GCF_900195285.2_Pc0421_3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:11,173] [INFO] Task started: fastANI
[2024-01-25 19:12:11,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9469d1-b4c5-4374-8415-2a15a34b1e7f/GCF_900195285.2_Pc0421_3_genomic.fna.gz --refList GCF_900195285.2_Pc0421_3_genomic.fna/target_genomes_gtdb.txt --output GCF_900195285.2_Pc0421_3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:21,019] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:21,026] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:21,026] [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_002307355.1	s__Pectobacterium polaris	96.0184	1305	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	conclusive
GCF_900129615.1	s__Pectobacterium carotovorum	93.5126	1251	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_000754695.1	s__Pectobacterium brasiliense	93.4719	1271	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_003382565.2	s__Pectobacterium aquaticum	93.1447	1143	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	93.0539	1181	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_000803315.1	s__Pectobacterium actinidiae	91.6534	1248	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_019056595.1	s__Pectobacterium atrosepticum	89.7329	1248	1533	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	89.6776	1242	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:21,027] [INFO] GTDB search result was written to GCF_900195285.2_Pc0421_3_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:21,028] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:21,031] [INFO] DFAST_QC result json was written to GCF_900195285.2_Pc0421_3_genomic.fna/dqc_result.json
[2024-01-25 19:12:21,031] [INFO] DFAST_QC completed!
[2024-01-25 19:12:21,031] [INFO] Total running time: 0h1m15s