[2024-01-24 12:45:20,769] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference
[2024-01-24 12:45:22,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:22,087] [INFO] Task started: Prodigal
[2024-01-24 12:45:22,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg40f4e922-19f8-4c35-8251-aaa853912e95/GCF_019048065.1_ASM1904806v1_genomic.fna.gz | prodigal -d GCF_019048065.1_ASM1904806v1_genomic.fna/cds.fna -a GCF_019048065.1_ASM1904806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:35,909] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:35,909] [INFO] Task started: HMMsearch
[2024-01-24 12:45:35,909] [INFO] Running command: hmmsearch --tblout GCF_019048065.1_ASM1904806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/reference_markers.hmm GCF_019048065.1_ASM1904806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:36,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:36,223] [INFO] Found 6/6 markers.
[2024-01-24 12:45:36,266] [INFO] Query marker FASTA was written to GCF_019048065.1_ASM1904806v1_genomic.fna/markers.fasta
[2024-01-24 12:45:36,267] [INFO] Task started: Blastn
[2024-01-24 12:45:36,267] [INFO] Running command: blastn -query GCF_019048065.1_ASM1904806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/reference_markers.fasta -out GCF_019048065.1_ASM1904806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:37,182] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:37,186] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:37,187] [INFO] Target genome list was writen to GCF_019048065.1_ASM1904806v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:37,200] [INFO] Task started: fastANI
[2024-01-24 12:45:37,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f4e922-19f8-4c35-8251-aaa853912e95/GCF_019048065.1_ASM1904806v1_genomic.fna.gz --refList GCF_019048065.1_ASM1904806v1_genomic.fna/target_genomes.txt --output GCF_019048065.1_ASM1904806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:50,630] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:50,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:50,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:50,646] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:50,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:50,647] [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 farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	100.0	1653	1654	95	conclusive
Citrobacter amalonaticus	strain=JCM 1661	GCA_018323885.1	35703	35703	type	True	91.5918	1398	1654	95	below_threshold
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	91.5159	1419	1654	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	84.9798	1144	1654	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	84.9234	1108	1654	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	83.4859	1111	1654	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.9141	974	1654	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	82.4814	965	1654	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	82.4046	887	1654	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	82.242	845	1654	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8926	874	1654	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.6776	882	1654	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:50,649] [INFO] DFAST Taxonomy check result was written to GCF_019048065.1_ASM1904806v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:50,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:50,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:50,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/checkm_data
[2024-01-24 12:45:50,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:50,698] [INFO] Task started: CheckM
[2024-01-24 12:45:50,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048065.1_ASM1904806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048065.1_ASM1904806v1_genomic.fna/checkm_input GCF_019048065.1_ASM1904806v1_genomic.fna/checkm_result
[2024-01-24 12:46:34,818] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:34,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:34,846] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:34,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:34,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048065.1_ASM1904806v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:34,847] [INFO] Task started: Blastn
[2024-01-24 12:46:34,847] [INFO] Running command: blastn -query GCF_019048065.1_ASM1904806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd70aa07-77ba-40f8-9b62-e9555d0df124/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048065.1_ASM1904806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:36,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:36,257] [INFO] Selected 5 target genomes.
[2024-01-24 12:46:36,258] [INFO] Target genome list was writen to GCF_019048065.1_ASM1904806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:36,271] [INFO] Task started: fastANI
[2024-01-24 12:46:36,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f4e922-19f8-4c35-8251-aaa853912e95/GCF_019048065.1_ASM1904806v1_genomic.fna.gz --refList GCF_019048065.1_ASM1904806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048065.1_ASM1904806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:43,612] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:43,622] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:43,622] [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_019048065.1	s__Citrobacter_A farmeri	100.0	1653	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.22	96.70	0.93	0.90	16	conclusive
GCF_009363175.1	s__Citrobacter_A telavivensis	93.7797	1501	1654	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	93.212	1458	1654	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_018323885.1	s__Citrobacter_A amalonaticus	91.5969	1399	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.67	95.02	0.91	0.83	59	-
GCF_018252635.1	s__Citrobacter_A amalonaticus_E	91.5414	1447	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:43,624] [INFO] GTDB search result was written to GCF_019048065.1_ASM1904806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:43,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:43,627] [INFO] DFAST_QC result json was written to GCF_019048065.1_ASM1904806v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:43,628] [INFO] DFAST_QC completed!
[2024-01-24 12:46:43,628] [INFO] Total running time: 0h1m23s