[2024-01-24 14:14:00,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference
[2024-01-24 14:14:02,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,036] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,036] [INFO] Running command: gunzip -c /var/lib/cwl/stgfddea522-4b2f-4d0e-aa1b-e4adda9638cc/GCF_001676155.1_ASM167615v1_genomic.fna.gz | prodigal -d GCF_001676155.1_ASM167615v1_genomic.fna/cds.fna -a GCF_001676155.1_ASM167615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:14,515] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:14,515] [INFO] Task started: HMMsearch
[2024-01-24 14:14:14,515] [INFO] Running command: hmmsearch --tblout GCF_001676155.1_ASM167615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/reference_markers.hmm GCF_001676155.1_ASM167615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:14,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:14,995] [INFO] Found 6/6 markers.
[2024-01-24 14:14:15,052] [INFO] Query marker FASTA was written to GCF_001676155.1_ASM167615v1_genomic.fna/markers.fasta
[2024-01-24 14:14:15,052] [INFO] Task started: Blastn
[2024-01-24 14:14:15,052] [INFO] Running command: blastn -query GCF_001676155.1_ASM167615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/reference_markers.fasta -out GCF_001676155.1_ASM167615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:16,345] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:16,350] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:16,350] [INFO] Target genome list was writen to GCF_001676155.1_ASM167615v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:16,380] [INFO] Task started: fastANI
[2024-01-24 14:14:16,381] [INFO] Running command: fastANI --query /var/lib/cwl/stgfddea522-4b2f-4d0e-aa1b-e4adda9638cc/GCF_001676155.1_ASM167615v1_genomic.fna.gz --refList GCF_001676155.1_ASM167615v1_genomic.fna/target_genomes.txt --output GCF_001676155.1_ASM167615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:33,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:33,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:33,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:33,652] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:33,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:33,653] [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
Morganella psychrotolerans	strain=GCSL-P101	GCA_001676155.1	368603	368603	type	True	100.0	1365	1365	95	conclusive
Morganella morganii	strain=DSM 30164	GCA_019243775.1	582	582	type	True	83.734	989	1365	95	below_threshold
Morganella morganii subsp. morganii	strain=ATCC 25830	GCA_006094455.1	180434	582	type	True	83.7065	978	1365	95	below_threshold
Morganella morganii subsp. morganii	strain=NBRC 3848	GCA_001598895.1	180434	582	type	True	83.7005	1008	1365	95	below_threshold
Moellerella wisconsensis	strain=NCTC12132	GCA_900706815.1	158849	158849	type	True	78.0995	150	1365	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	77.8435	150	1365	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	77.803	184	1365	95	below_threshold
Yersinia entomophaga	strain=MH96	GCA_001656035.1	935293	935293	type	True	77.5826	170	1365	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	77.5791	163	1365	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	77.579	176	1365	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.5194	198	1365	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	77.4927	187	1365	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	77.4698	169	1365	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	77.4097	171	1365	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.2992	205	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:33,657] [INFO] DFAST Taxonomy check result was written to GCF_001676155.1_ASM167615v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:33,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:33,658] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:33,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/checkm_data
[2024-01-24 14:14:33,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:33,706] [INFO] Task started: CheckM
[2024-01-24 14:14:33,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001676155.1_ASM167615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001676155.1_ASM167615v1_genomic.fna/checkm_input GCF_001676155.1_ASM167615v1_genomic.fna/checkm_result
[2024-01-24 14:15:10,380] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:10,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:10,408] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:10,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:10,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001676155.1_ASM167615v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:10,409] [INFO] Task started: Blastn
[2024-01-24 14:15:10,409] [INFO] Running command: blastn -query GCF_001676155.1_ASM167615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd37fd7ea-ccb1-4584-973f-37b40dbd783d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001676155.1_ASM167615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:11,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:11,650] [INFO] Selected 6 target genomes.
[2024-01-24 14:15:11,650] [INFO] Target genome list was writen to GCF_001676155.1_ASM167615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:11,657] [INFO] Task started: fastANI
[2024-01-24 14:15:11,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgfddea522-4b2f-4d0e-aa1b-e4adda9638cc/GCF_001676155.1_ASM167615v1_genomic.fna.gz --refList GCF_001676155.1_ASM167615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001676155.1_ASM167615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:18,584] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:18,597] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:18,597] [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_001676155.1	s__Morganella psychrotolerans	100.0	1365	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.64	95.31	0.94	0.87	3	conclusive
GCF_001676055.1	s__Morganella psychrotolerans_B	93.3615	1172	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	95.92	95.92	0.88	0.88	2	-
GCF_019243775.1	s__Morganella morganii	83.7312	989	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	98.34	95.47	0.94	0.88	171	-
GCF_000633515.1	s__Morganella morganii_B	83.5255	988	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	96.84	95.81	0.92	0.90	4	-
GCF_003996855.1	s__Morganella morganii_C	83.4424	950	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019242955.1	s__Morganella morganii_A	83.3977	1032	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.48	97.24	0.94	0.90	21	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:18,599] [INFO] GTDB search result was written to GCF_001676155.1_ASM167615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:18,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:18,606] [INFO] DFAST_QC result json was written to GCF_001676155.1_ASM167615v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:18,606] [INFO] DFAST_QC completed!
[2024-01-24 14:15:18,607] [INFO] Total running time: 0h1m18s