[2024-01-24 14:28:02,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference
[2024-01-24 14:28:04,079] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,080] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbf4ca1a-e289-4aff-9054-9a4b5304f7e2/GCF_000754765.1_ASM75476v1_genomic.fna.gz | prodigal -d GCF_000754765.1_ASM75476v1_genomic.fna/cds.fna -a GCF_000754765.1_ASM75476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:17,376] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:17,376] [INFO] Task started: HMMsearch
[2024-01-24 14:28:17,376] [INFO] Running command: hmmsearch --tblout GCF_000754765.1_ASM75476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/reference_markers.hmm GCF_000754765.1_ASM75476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:17,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:17,714] [INFO] Found 6/6 markers.
[2024-01-24 14:28:17,790] [INFO] Query marker FASTA was written to GCF_000754765.1_ASM75476v1_genomic.fna/markers.fasta
[2024-01-24 14:28:17,790] [INFO] Task started: Blastn
[2024-01-24 14:28:17,791] [INFO] Running command: blastn -query GCF_000754765.1_ASM75476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/reference_markers.fasta -out GCF_000754765.1_ASM75476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:18,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:18,764] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:18,764] [INFO] Target genome list was writen to GCF_000754765.1_ASM75476v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:18,797] [INFO] Task started: fastANI
[2024-01-24 14:28:18,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf4ca1a-e289-4aff-9054-9a4b5304f7e2/GCF_000754765.1_ASM75476v1_genomic.fna.gz --refList GCF_000754765.1_ASM75476v1_genomic.fna/target_genomes.txt --output GCF_000754765.1_ASM75476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,556] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,571] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:28:40,571] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:28:40,571] [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 odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	100.0	1631	1635	95	inconclusive
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	95.224	1346	1635	95	inconclusive
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	95.2225	1350	1635	95	inconclusive
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	95.2073	1355	1635	95	inconclusive
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	95.1304	1325	1635	95	inconclusive
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	93.2699	1194	1635	95	below_threshold
Pectobacterium actinidiae	strain=KKH3	GCA_000803315.1	1507808	1507808	type	True	92.9093	1327	1635	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	92.8779	1247	1635	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	92.8442	1316	1635	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	92.3421	1316	1635	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	92.3091	1326	1635	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	92.2413	1210	1635	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.133	1304	1635	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.7837	406	1635	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5549	425	1635	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.3837	412	1635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,573] [INFO] DFAST Taxonomy check result was written to GCF_000754765.1_ASM75476v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,574] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/checkm_data
[2024-01-24 14:28:40,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:40,627] [INFO] Task started: CheckM
[2024-01-24 14:28:40,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000754765.1_ASM75476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000754765.1_ASM75476v1_genomic.fna/checkm_input GCF_000754765.1_ASM75476v1_genomic.fna/checkm_result
[2024-01-24 14:29:24,540] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:24,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:24,563] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:24,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:24,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000754765.1_ASM75476v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:24,564] [INFO] Task started: Blastn
[2024-01-24 14:29:24,565] [INFO] Running command: blastn -query GCF_000754765.1_ASM75476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95f1bd22-8e31-48de-bc4a-2888e4a87ab5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000754765.1_ASM75476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:25,960] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:25,964] [INFO] Selected 8 target genomes.
[2024-01-24 14:29:25,965] [INFO] Target genome list was writen to GCF_000754765.1_ASM75476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:25,976] [INFO] Task started: fastANI
[2024-01-24 14:29:25,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf4ca1a-e289-4aff-9054-9a4b5304f7e2/GCF_000754765.1_ASM75476v1_genomic.fna.gz --refList GCF_000754765.1_ASM75476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000754765.1_ASM75476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:36,512] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:36,528] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:36,529] [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_900129615.1	s__Pectobacterium carotovorum	95.2225	1350	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	conclusive
GCF_003382565.2	s__Pectobacterium aquaticum	93.3804	1164	1635	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	92.8971	1328	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_002307355.1	s__Pectobacterium polaris	92.8373	1317	1635	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	92.3335	1317	1635	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	92.1023	1235	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_002847345.1	s__Pectobacterium peruviense	89.725	1289	1635	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	89.1952	1209	1635	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 14:29:36,531] [INFO] GTDB search result was written to GCF_000754765.1_ASM75476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:36,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:36,537] [INFO] DFAST_QC result json was written to GCF_000754765.1_ASM75476v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:36,537] [INFO] DFAST_QC completed!
[2024-01-24 14:29:36,537] [INFO] Total running time: 0h1m34s