[2024-01-24 14:22:03,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference
[2024-01-24 14:22:05,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,159] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,159] [INFO] Running command: gunzip -c /var/lib/cwl/stgd886a11f-090d-4658-aad8-a1fe63e29e27/GCF_011064845.1_ASM1106484v1_genomic.fna.gz | prodigal -d GCF_011064845.1_ASM1106484v1_genomic.fna/cds.fna -a GCF_011064845.1_ASM1106484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:19,317] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:19,317] [INFO] Task started: HMMsearch
[2024-01-24 14:22:19,317] [INFO] Running command: hmmsearch --tblout GCF_011064845.1_ASM1106484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/reference_markers.hmm GCF_011064845.1_ASM1106484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:19,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:19,647] [INFO] Found 6/6 markers.
[2024-01-24 14:22:19,689] [INFO] Query marker FASTA was written to GCF_011064845.1_ASM1106484v1_genomic.fna/markers.fasta
[2024-01-24 14:22:19,689] [INFO] Task started: Blastn
[2024-01-24 14:22:19,690] [INFO] Running command: blastn -query GCF_011064845.1_ASM1106484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/reference_markers.fasta -out GCF_011064845.1_ASM1106484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:20,684] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:20,688] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:20,688] [INFO] Target genome list was writen to GCF_011064845.1_ASM1106484v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:20,699] [INFO] Task started: fastANI
[2024-01-24 14:22:20,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgd886a11f-090d-4658-aad8-a1fe63e29e27/GCF_011064845.1_ASM1106484v1_genomic.fna.gz --refList GCF_011064845.1_ASM1106484v1_genomic.fna/target_genomes.txt --output GCF_011064845.1_ASM1106484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:34,084] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:34,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:34,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:34,094] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:22:34,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:34,095] [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
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	100.0	1652	1652	95	conclusive
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	99.9723	1611	1652	95	conclusive
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	99.9721	1603	1652	95	conclusive
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	99.9242	1558	1652	95	conclusive
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	94.7135	1391	1652	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	92.5876	1441	1652	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	83.1327	966	1652	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.9961	1037	1652	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	82.0276	840	1652	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.731	852	1652	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6918	854	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:34,096] [INFO] DFAST Taxonomy check result was written to GCF_011064845.1_ASM1106484v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:34,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:34,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:34,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/checkm_data
[2024-01-24 14:22:34,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:34,146] [INFO] Task started: CheckM
[2024-01-24 14:22:34,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011064845.1_ASM1106484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011064845.1_ASM1106484v1_genomic.fna/checkm_input GCF_011064845.1_ASM1106484v1_genomic.fna/checkm_result
[2024-01-24 14:23:16,464] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:16,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:16,488] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:16,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:16,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011064845.1_ASM1106484v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:16,489] [INFO] Task started: Blastn
[2024-01-24 14:23:16,489] [INFO] Running command: blastn -query GCF_011064845.1_ASM1106484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01a151d0-9ed4-4bf4-8db9-dbb95f98e483/dqc_reference/reference_markers_gtdb.fasta -out GCF_011064845.1_ASM1106484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:18,013] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:18,018] [INFO] Selected 8 target genomes.
[2024-01-24 14:23:18,019] [INFO] Target genome list was writen to GCF_011064845.1_ASM1106484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:18,028] [INFO] Task started: fastANI
[2024-01-24 14:23:18,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgd886a11f-090d-4658-aad8-a1fe63e29e27/GCF_011064845.1_ASM1106484v1_genomic.fna.gz --refList GCF_011064845.1_ASM1106484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011064845.1_ASM1106484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:27,543] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:27,555] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:27,555] [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_011064845.1	s__Citrobacter freundii	100.0	1651	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	conclusive
GCF_002042885.1	s__Citrobacter portucalensis	94.7135	1391	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_900079995.3	s__Citrobacter europaeus	92.752	1421	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
GCF_018035235.1	s__Citrobacter freundii_A	92.7505	1367	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_004353845.1	s__Citrobacter freundii_E	92.5876	1441	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002075345.1	s__Citrobacter braakii	92.3557	1371	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_003818115.1	s__Citrobacter youngae	91.7226	1340	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCA_900759445.1	s__Klebsiella sp900759445	86.5843	728	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:27,557] [INFO] GTDB search result was written to GCF_011064845.1_ASM1106484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:27,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:27,562] [INFO] DFAST_QC result json was written to GCF_011064845.1_ASM1106484v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:27,562] [INFO] DFAST_QC completed!
[2024-01-24 14:23:27,562] [INFO] Total running time: 0h1m24s