[2023-06-27 18:55:48,994] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:55:48,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:55:48,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference
[2023-06-27 18:55:50,220] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:55:50,221] [INFO] Task started: Prodigal
[2023-06-27 18:55:50,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg27567ab0-19c9-4dc1-b0ba-1314711720f1/GCA_002322335.1_ASM232233v1_genomic.fna.gz | prodigal -d GCA_002322335.1_ASM232233v1_genomic.fna/cds.fna -a GCA_002322335.1_ASM232233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:55:59,993] [INFO] Task succeeded: Prodigal
[2023-06-27 18:55:59,994] [INFO] Task started: HMMsearch
[2023-06-27 18:55:59,994] [INFO] Running command: hmmsearch --tblout GCA_002322335.1_ASM232233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/reference_markers.hmm GCA_002322335.1_ASM232233v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:56:00,335] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:56:00,336] [INFO] Found 6/6 markers.
[2023-06-27 18:56:00,375] [INFO] Query marker FASTA was written to GCA_002322335.1_ASM232233v1_genomic.fna/markers.fasta
[2023-06-27 18:56:00,376] [INFO] Task started: Blastn
[2023-06-27 18:56:00,376] [INFO] Running command: blastn -query GCA_002322335.1_ASM232233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/reference_markers.fasta -out GCA_002322335.1_ASM232233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:01,228] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:01,232] [INFO] Selected 23 target genomes.
[2023-06-27 18:56:01,233] [INFO] Target genome list was writen to GCA_002322335.1_ASM232233v1_genomic.fna/target_genomes.txt
[2023-06-27 18:56:01,267] [INFO] Task started: fastANI
[2023-06-27 18:56:01,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg27567ab0-19c9-4dc1-b0ba-1314711720f1/GCA_002322335.1_ASM232233v1_genomic.fna.gz --refList GCA_002322335.1_ASM232233v1_genomic.fna/target_genomes.txt --output GCA_002322335.1_ASM232233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:56:21,793] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:21,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:56:21,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:56:21,810] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:56:21,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:56:21,811] [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
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	86.2265	921	1205	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	86.1579	937	1205	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	81.4415	659	1205	95	below_threshold
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	81.4077	666	1205	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	81.364	653	1205	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	81.3247	624	1205	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	81.3052	662	1205	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	81.187	633	1205	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	81.1853	662	1205	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	81.1427	625	1205	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	81.125	642	1205	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	81.1105	635	1205	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	81.0348	612	1205	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.9803	630	1205	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	80.917	617	1205	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.9131	645	1205	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	80.8897	619	1205	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	80.6505	593	1205	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	80.5632	599	1205	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.5503	638	1205	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.4669	608	1205	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	80.3529	576	1205	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	80.2464	592	1205	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:56:21,813] [INFO] DFAST Taxonomy check result was written to GCA_002322335.1_ASM232233v1_genomic.fna/tc_result.tsv
[2023-06-27 18:56:21,813] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:56:21,814] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:56:21,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/checkm_data
[2023-06-27 18:56:21,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:56:21,861] [INFO] Task started: CheckM
[2023-06-27 18:56:21,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002322335.1_ASM232233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002322335.1_ASM232233v1_genomic.fna/checkm_input GCA_002322335.1_ASM232233v1_genomic.fna/checkm_result
[2023-06-27 18:56:54,784] [INFO] Task succeeded: CheckM
[2023-06-27 18:56:54,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:56:54,819] [INFO] ===== Completeness check finished =====
[2023-06-27 18:56:54,820] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:56:54,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002322335.1_ASM232233v1_genomic.fna/markers.fasta)
[2023-06-27 18:56:54,821] [INFO] Task started: Blastn
[2023-06-27 18:56:54,821] [INFO] Running command: blastn -query GCA_002322335.1_ASM232233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0946155f-bf04-48cc-9208-8d583e7ddc15/dqc_reference/reference_markers_gtdb.fasta -out GCA_002322335.1_ASM232233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:55,995] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:56,000] [INFO] Selected 6 target genomes.
[2023-06-27 18:56:56,000] [INFO] Target genome list was writen to GCA_002322335.1_ASM232233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:56:56,004] [INFO] Task started: fastANI
[2023-06-27 18:56:56,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg27567ab0-19c9-4dc1-b0ba-1314711720f1/GCA_002322335.1_ASM232233v1_genomic.fna.gz --refList GCA_002322335.1_ASM232233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002322335.1_ASM232233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:57:02,041] [INFO] Task succeeded: fastANI
[2023-06-27 18:57:02,052] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:57:02,052] [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_007570865.1	s__Atlantibacter subterranea	98.4532	1098	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	conclusive
GCF_009907385.1	s__Atlantibacter hermannii_A	94.1231	1009	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193285.1	s__Atlantibacter sp002345315	92.429	1026	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCA_900635495.1	s__Atlantibacter hermannii	86.1972	928	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
GCF_011077955.1	s__Atlantibacter sp002358165	85.2605	877	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	99.01	98.64	0.96	0.94	5	-
GCF_003057745.1	s__Enterobacter sp003057745	80.8677	627	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:57:02,054] [INFO] GTDB search result was written to GCA_002322335.1_ASM232233v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:57:02,054] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:57:02,059] [INFO] DFAST_QC result json was written to GCA_002322335.1_ASM232233v1_genomic.fna/dqc_result.json
[2023-06-27 18:57:02,059] [INFO] DFAST_QC completed!
[2023-06-27 18:57:02,059] [INFO] Total running time: 0h1m13s