[2024-01-24 12:30:48,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,676] [INFO] DQC Reference Directory: /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference
[2024-01-24 12:30:50,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,062] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f2a7e79-977e-471f-b12e-4c67cfe315b7/GCF_020099335.1_ASM2009933v1_genomic.fna.gz | prodigal -d GCF_020099335.1_ASM2009933v1_genomic.fna/cds.fna -a GCF_020099335.1_ASM2009933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:04,030] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:04,030] [INFO] Task started: HMMsearch
[2024-01-24 12:31:04,030] [INFO] Running command: hmmsearch --tblout GCF_020099335.1_ASM2009933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/reference_markers.hmm GCF_020099335.1_ASM2009933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:04,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:04,418] [INFO] Found 6/6 markers.
[2024-01-24 12:31:04,464] [INFO] Query marker FASTA was written to GCF_020099335.1_ASM2009933v1_genomic.fna/markers.fasta
[2024-01-24 12:31:04,464] [INFO] Task started: Blastn
[2024-01-24 12:31:04,465] [INFO] Running command: blastn -query GCF_020099335.1_ASM2009933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/reference_markers.fasta -out GCF_020099335.1_ASM2009933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:05,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:05,334] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:05,335] [INFO] Target genome list was writen to GCF_020099335.1_ASM2009933v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:05,341] [INFO] Task started: fastANI
[2024-01-24 12:31:05,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2a7e79-977e-471f-b12e-4c67cfe315b7/GCF_020099335.1_ASM2009933v1_genomic.fna.gz --refList GCF_020099335.1_ASM2009933v1_genomic.fna/target_genomes.txt --output GCF_020099335.1_ASM2009933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:18,364] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:18,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:18,374] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:18,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:18,374] [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 amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	100.0	1687	1688	95	conclusive
Citrobacter amalonaticus	strain=JCM 1661	GCA_018323885.1	35703	35703	type	True	99.9963	1681	1688	95	conclusive
Citrobacter farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	91.5816	1407	1688	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	84.9653	1155	1688	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	84.892	1124	1688	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.7713	985	1688	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.914	900	1688	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7992	915	1688	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.7671	889	1688	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	80.8834	894	1688	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	80.8472	879	1688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,376] [INFO] DFAST Taxonomy check result was written to GCF_020099335.1_ASM2009933v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:18,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:18,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:18,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/checkm_data
[2024-01-24 12:31:18,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:18,434] [INFO] Task started: CheckM
[2024-01-24 12:31:18,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020099335.1_ASM2009933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020099335.1_ASM2009933v1_genomic.fna/checkm_input GCF_020099335.1_ASM2009933v1_genomic.fna/checkm_result
[2024-01-24 12:32:03,009] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:03,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:03,040] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:03,040] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:03,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020099335.1_ASM2009933v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:03,041] [INFO] Task started: Blastn
[2024-01-24 12:32:03,041] [INFO] Running command: blastn -query GCF_020099335.1_ASM2009933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6a724ec-1153-4606-8029-96c74050fa3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020099335.1_ASM2009933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:04,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:04,218] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:04,218] [INFO] Target genome list was writen to GCF_020099335.1_ASM2009933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:04,226] [INFO] Task started: fastANI
[2024-01-24 12:32:04,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2a7e79-977e-471f-b12e-4c67cfe315b7/GCF_020099335.1_ASM2009933v1_genomic.fna.gz --refList GCF_020099335.1_ASM2009933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020099335.1_ASM2009933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:14,193] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:14,204] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:14,204] [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_018323885.1	s__Citrobacter_A amalonaticus	99.9963	1681	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.67	95.02	0.91	0.83	59	conclusive
GCF_018252635.1	s__Citrobacter_A amalonaticus_E	92.6193	1403	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363175.1	s__Citrobacter_A telavivensis	91.7808	1429	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000981805.1	s__Citrobacter_A amalonaticus_C	91.7618	1418	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048065.1	s__Citrobacter_A farmeri	91.5694	1408	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.22	96.70	0.93	0.90	16	-
GCF_000734965.1	s__Trabulsiella guamensis	81.124	832	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001756855.1	s__Erwinia dacicola	79.1374	196	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_001187905.1	s__Pantoea sp001187905	78.2479	433	1688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:14,206] [INFO] GTDB search result was written to GCF_020099335.1_ASM2009933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:14,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:14,210] [INFO] DFAST_QC result json was written to GCF_020099335.1_ASM2009933v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:14,210] [INFO] DFAST_QC completed!
[2024-01-24 12:32:14,210] [INFO] Total running time: 0h1m26s