[2024-01-25 19:46:50,535] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:50,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:50,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference
[2024-01-25 19:46:51,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:51,754] [INFO] Task started: Prodigal
[2024-01-25 19:46:51,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b8e4b8f-ea80-45d5-8883-2174df2264ef/GCF_001729745.1_ASM172974v1_genomic.fna.gz | prodigal -d GCF_001729745.1_ASM172974v1_genomic.fna/cds.fna -a GCF_001729745.1_ASM172974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:03,053] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:03,054] [INFO] Task started: HMMsearch
[2024-01-25 19:47:03,054] [INFO] Running command: hmmsearch --tblout GCF_001729745.1_ASM172974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/reference_markers.hmm GCF_001729745.1_ASM172974v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:03,333] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:03,334] [INFO] Found 6/6 markers.
[2024-01-25 19:47:03,373] [INFO] Query marker FASTA was written to GCF_001729745.1_ASM172974v1_genomic.fna/markers.fasta
[2024-01-25 19:47:03,374] [INFO] Task started: Blastn
[2024-01-25 19:47:03,374] [INFO] Running command: blastn -query GCF_001729745.1_ASM172974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/reference_markers.fasta -out GCF_001729745.1_ASM172974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:04,243] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:04,245] [INFO] Selected 12 target genomes.
[2024-01-25 19:47:04,246] [INFO] Target genome list was writen to GCF_001729745.1_ASM172974v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:04,250] [INFO] Task started: fastANI
[2024-01-25 19:47:04,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b8e4b8f-ea80-45d5-8883-2174df2264ef/GCF_001729745.1_ASM172974v1_genomic.fna.gz --refList GCF_001729745.1_ASM172974v1_genomic.fna/target_genomes.txt --output GCF_001729745.1_ASM172974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:18,616] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:18,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:18,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:18,625] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:47:18,625] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:18,626] [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
Enterobacter hormaechei subsp. hoffmannii	strain=DSM 14563	GCA_001729745.1	1812934	158836	type	True	100.0	1557	1558	95	conclusive
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	95.9983	1392	1558	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	95.9747	1379	1558	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	95.9304	1389	1558	95	conclusive
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	95.921	1408	1558	95	conclusive
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	94.5553	1370	1558	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	94.4908	1376	1558	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_000213995.1	301105	158836	type	True	94.4891	1346	1558	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	88.2913	1199	1558	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.1004	1273	1558	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	87.6133	1227	1558	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	87.489	1275	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,627] [INFO] DFAST Taxonomy check result was written to GCF_001729745.1_ASM172974v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:18,627] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:18,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:18,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/checkm_data
[2024-01-25 19:47:18,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:18,672] [INFO] Task started: CheckM
[2024-01-25 19:47:18,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001729745.1_ASM172974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001729745.1_ASM172974v1_genomic.fna/checkm_input GCF_001729745.1_ASM172974v1_genomic.fna/checkm_result
[2024-01-25 19:47:54,220] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:54,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:54,235] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:54,235] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:54,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001729745.1_ASM172974v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:54,236] [INFO] Task started: Blastn
[2024-01-25 19:47:54,236] [INFO] Running command: blastn -query GCF_001729745.1_ASM172974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3834dc88-8f8f-4caf-94ed-e014223a7b08/dqc_reference/reference_markers_gtdb.fasta -out GCF_001729745.1_ASM172974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:55,684] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:55,686] [INFO] Selected 7 target genomes.
[2024-01-25 19:47:55,686] [INFO] Target genome list was writen to GCF_001729745.1_ASM172974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:55,692] [INFO] Task started: fastANI
[2024-01-25 19:47:55,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b8e4b8f-ea80-45d5-8883-2174df2264ef/GCF_001729745.1_ASM172974v1_genomic.fna.gz --refList GCF_001729745.1_ASM172974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001729745.1_ASM172974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:05,180] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:05,187] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:05,187] [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_001729745.1	s__Enterobacter hormaechei_A	100.0	1558	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	conclusive
GCF_001875655.1	s__Enterobacter hormaechei	94.554	1370	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	-
GCF_011078175.1	s__Enterobacter cloacae_Q	94.2892	1306	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900322725.1	s__Enterobacter quasihormaechei	93.7489	1367	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_013375935.1	s__Enterobacter cloacae_O	91.5119	1358	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_011754535.1	s__Enterobacter cloacae_N	88.5988	1291	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_009755685.1	s__Enterobacter sp000568095	88.1848	1254	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:05,188] [INFO] GTDB search result was written to GCF_001729745.1_ASM172974v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:05,189] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:05,191] [INFO] DFAST_QC result json was written to GCF_001729745.1_ASM172974v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:05,191] [INFO] DFAST_QC completed!
[2024-01-25 19:48:05,192] [INFO] Total running time: 0h1m15s