[2024-01-25 17:49:05,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:05,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:05,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference
[2024-01-25 17:49:06,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:06,805] [INFO] Task started: Prodigal
[2024-01-25 17:49:06,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgb738ddfc-8cf5-4ada-9986-44049f8e3a7d/GCF_026800125.1_ASM2680012v1_genomic.fna.gz | prodigal -d GCF_026800125.1_ASM2680012v1_genomic.fna/cds.fna -a GCF_026800125.1_ASM2680012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:19,248] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:19,248] [INFO] Task started: HMMsearch
[2024-01-25 17:49:19,249] [INFO] Running command: hmmsearch --tblout GCF_026800125.1_ASM2680012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/reference_markers.hmm GCF_026800125.1_ASM2680012v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:19,552] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:19,553] [INFO] Found 6/6 markers.
[2024-01-25 17:49:19,597] [INFO] Query marker FASTA was written to GCF_026800125.1_ASM2680012v1_genomic.fna/markers.fasta
[2024-01-25 17:49:19,597] [INFO] Task started: Blastn
[2024-01-25 17:49:19,597] [INFO] Running command: blastn -query GCF_026800125.1_ASM2680012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/reference_markers.fasta -out GCF_026800125.1_ASM2680012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:20,395] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:20,398] [INFO] Selected 14 target genomes.
[2024-01-25 17:49:20,399] [INFO] Target genome list was writen to GCF_026800125.1_ASM2680012v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:20,409] [INFO] Task started: fastANI
[2024-01-25 17:49:20,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgb738ddfc-8cf5-4ada-9986-44049f8e3a7d/GCF_026800125.1_ASM2680012v1_genomic.fna.gz --refList GCF_026800125.1_ASM2680012v1_genomic.fna/target_genomes.txt --output GCF_026800125.1_ASM2680012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:35,346] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:35,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:35,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:35,355] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:35,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:35,355] [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 brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	94.6218	1392	1666	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	94.6202	1418	1666	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	93.6956	1394	1666	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	93.6933	1397	1666	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	93.6774	1401	1666	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	93.3772	1251	1666	95	below_threshold
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	93.3556	1399	1666	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.6357	1331	1666	95	below_threshold
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	89.6604	1302	1666	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.3978	421	1666	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.3907	417	1666	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.3032	392	1666	95	below_threshold
Proteus mirabilis	strain=ATCC 29906	GCA_000160755.1	584	584	type	True	77.8394	85	1666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:35,357] [INFO] DFAST Taxonomy check result was written to GCF_026800125.1_ASM2680012v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:35,357] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:35,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:35,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/checkm_data
[2024-01-25 17:49:35,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:35,414] [INFO] Task started: CheckM
[2024-01-25 17:49:35,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026800125.1_ASM2680012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026800125.1_ASM2680012v1_genomic.fna/checkm_input GCF_026800125.1_ASM2680012v1_genomic.fna/checkm_result
[2024-01-25 17:50:15,719] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:15,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:15,761] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:15,762] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:15,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026800125.1_ASM2680012v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:15,764] [INFO] Task started: Blastn
[2024-01-25 17:50:15,764] [INFO] Running command: blastn -query GCF_026800125.1_ASM2680012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b76fba-b242-4ec1-ae17-9526a7971b81/dqc_reference/reference_markers_gtdb.fasta -out GCF_026800125.1_ASM2680012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:16,935] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:16,938] [INFO] Selected 11 target genomes.
[2024-01-25 17:50:16,938] [INFO] Target genome list was writen to GCF_026800125.1_ASM2680012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:16,949] [INFO] Task started: fastANI
[2024-01-25 17:50:16,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgb738ddfc-8cf5-4ada-9986-44049f8e3a7d/GCF_026800125.1_ASM2680012v1_genomic.fna.gz --refList GCF_026800125.1_ASM2680012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026800125.1_ASM2680012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:30,745] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:30,752] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:30,752] [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	95.0864	1412	1666	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_000754695.1	s__Pectobacterium brasiliense	94.601	1394	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	93.8764	1258	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_900129615.1	s__Pectobacterium carotovorum	93.6774	1401	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_003382565.2	s__Pectobacterium aquaticum	93.0518	1200	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_000803315.1	s__Pectobacterium actinidiae	91.9092	1370	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_013449375.1	s__Pectobacterium sp013449375	90.8151	1244	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689195.1	s__Pectobacterium aroidearum	90.787	1390	1666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.07	97.92	0.91	0.90	12	-
GCF_005497185.1	s__Pectobacterium polonicum	89.7836	1335	1666	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	89.7184	1359	1666	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	89.7108	1369	1666	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 17:50:30,754] [INFO] GTDB search result was written to GCF_026800125.1_ASM2680012v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:30,755] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:30,757] [INFO] DFAST_QC result json was written to GCF_026800125.1_ASM2680012v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:30,757] [INFO] DFAST_QC completed!
[2024-01-25 17:50:30,757] [INFO] Total running time: 0h1m25s