[2024-01-24 12:13:43,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:43,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:43,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference
[2024-01-24 12:13:45,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:45,244] [INFO] Task started: Prodigal
[2024-01-24 12:13:45,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg2140503e-6490-4f84-a564-2d9643fb592d/GCF_019243775.1_ASM1924377v1_genomic.fna.gz | prodigal -d GCF_019243775.1_ASM1924377v1_genomic.fna/cds.fna -a GCF_019243775.1_ASM1924377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:55,419] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:55,419] [INFO] Task started: HMMsearch
[2024-01-24 12:13:55,419] [INFO] Running command: hmmsearch --tblout GCF_019243775.1_ASM1924377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/reference_markers.hmm GCF_019243775.1_ASM1924377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:55,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:55,818] [INFO] Found 6/6 markers.
[2024-01-24 12:13:55,864] [INFO] Query marker FASTA was written to GCF_019243775.1_ASM1924377v1_genomic.fna/markers.fasta
[2024-01-24 12:13:55,864] [INFO] Task started: Blastn
[2024-01-24 12:13:55,864] [INFO] Running command: blastn -query GCF_019243775.1_ASM1924377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/reference_markers.fasta -out GCF_019243775.1_ASM1924377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:56,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:56,801] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:56,802] [INFO] Target genome list was writen to GCF_019243775.1_ASM1924377v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:56,808] [INFO] Task started: fastANI
[2024-01-24 12:13:56,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg2140503e-6490-4f84-a564-2d9643fb592d/GCF_019243775.1_ASM1924377v1_genomic.fna.gz --refList GCF_019243775.1_ASM1924377v1_genomic.fna/target_genomes.txt --output GCF_019243775.1_ASM1924377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,412] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,426] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:14:12,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:12,426] [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 morganii	strain=DSM 30164	GCA_019243775.1	582	582	type	True	100.0	1271	1271	95	conclusive
Morganella morganii subsp. morganii	strain=NBRC 3848	GCA_001598895.1	180434	582	type	True	99.966	1247	1271	95	conclusive
Morganella morganii subsp. morganii	strain=ATCC 25830	GCA_006094455.1	180434	582	type	True	98.8259	1211	1271	95	conclusive
Morganella psychrotolerans	strain=GCSL-P101	GCA_001676155.1	368603	368603	type	True	83.8236	985	1271	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	78.4616	242	1271	95	below_threshold
Klebsiella huaxiensis	strain=WCHKl090001	GCA_003261575.2	2153354	2153354	type	True	78.4509	249	1271	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.3222	255	1271	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	78.2031	242	1271	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	78.1549	250	1271	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.0678	253	1271	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.0412	249	1271	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	77.9535	215	1271	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	77.7243	223	1271	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.5998	266	1271	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	77.5458	238	1271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,431] [INFO] DFAST Taxonomy check result was written to GCF_019243775.1_ASM1924377v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/checkm_data
[2024-01-24 12:14:12,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,493] [INFO] Task started: CheckM
[2024-01-24 12:14:12,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019243775.1_ASM1924377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019243775.1_ASM1924377v1_genomic.fna/checkm_input GCF_019243775.1_ASM1924377v1_genomic.fna/checkm_result
[2024-01-24 12:14:48,437] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:48,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:48,462] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:48,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:48,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019243775.1_ASM1924377v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:48,463] [INFO] Task started: Blastn
[2024-01-24 12:14:48,464] [INFO] Running command: blastn -query GCF_019243775.1_ASM1924377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc75a8e61-39c6-41a4-920b-de0933ea69ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_019243775.1_ASM1924377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,843] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,848] [INFO] Selected 6 target genomes.
[2024-01-24 12:14:49,848] [INFO] Target genome list was writen to GCF_019243775.1_ASM1924377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:49,854] [INFO] Task started: fastANI
[2024-01-24 12:14:49,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg2140503e-6490-4f84-a564-2d9643fb592d/GCF_019243775.1_ASM1924377v1_genomic.fna.gz --refList GCF_019243775.1_ASM1924377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019243775.1_ASM1924377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:56,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:56,530] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:56,530] [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_019243775.1	s__Morganella morganii	100.0	1271	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	98.34	95.47	0.94	0.88	171	conclusive
GCF_000633515.1	s__Morganella morganii_B	94.0567	1114	1271	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	92.1078	1065	1271	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	92.016	1137	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.48	97.24	0.94	0.90	21	-
GCF_001676055.1	s__Morganella psychrotolerans_B	83.8886	1001	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	95.92	95.92	0.88	0.88	2	-
GCF_001676155.1	s__Morganella psychrotolerans	83.8144	986	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.64	95.31	0.94	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,533] [INFO] GTDB search result was written to GCF_019243775.1_ASM1924377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:56,533] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:56,537] [INFO] DFAST_QC result json was written to GCF_019243775.1_ASM1924377v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:56,537] [INFO] DFAST_QC completed!
[2024-01-24 12:14:56,537] [INFO] Total running time: 0h1m13s