[2024-01-24 13:25:47,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference
[2024-01-24 13:25:49,196] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,197] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,197] [INFO] Running command: gunzip -c /var/lib/cwl/stgc516e376-722e-4e20-8257-f8be52bef313/GCF_900450975.1_29859_B01_genomic.fna.gz | prodigal -d GCF_900450975.1_29859_B01_genomic.fna/cds.fna -a GCF_900450975.1_29859_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:01,137] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:01,138] [INFO] Task started: HMMsearch
[2024-01-24 13:26:01,138] [INFO] Running command: hmmsearch --tblout GCF_900450975.1_29859_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/reference_markers.hmm GCF_900450975.1_29859_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:01,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:01,443] [INFO] Found 6/6 markers.
[2024-01-24 13:26:01,483] [INFO] Query marker FASTA was written to GCF_900450975.1_29859_B01_genomic.fna/markers.fasta
[2024-01-24 13:26:01,484] [INFO] Task started: Blastn
[2024-01-24 13:26:01,484] [INFO] Running command: blastn -query GCF_900450975.1_29859_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/reference_markers.fasta -out GCF_900450975.1_29859_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:02,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:02,367] [INFO] Selected 27 target genomes.
[2024-01-24 13:26:02,368] [INFO] Target genome list was writen to GCF_900450975.1_29859_B01_genomic.fna/target_genomes.txt
[2024-01-24 13:26:02,377] [INFO] Task started: fastANI
[2024-01-24 13:26:02,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgc516e376-722e-4e20-8257-f8be52bef313/GCF_900450975.1_29859_B01_genomic.fna.gz --refList GCF_900450975.1_29859_B01_genomic.fna/target_genomes.txt --output GCF_900450975.1_29859_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:28,732] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:28,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:28,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:28,752] [INFO] Found 27 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:28,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:28,752] [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
Pseudescherichia vulneris	strain=NCTC12130	GCA_900450975.1	566	566	type	True	100.0	1478	1479	95	conclusive
Pseudescherichia vulneris	strain=NBRC 102420	GCA_000759795.1	566	566	type	True	99.961	1425	1479	95	conclusive
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.2281	884	1479	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	82.1702	883	1479	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	82.1664	920	1479	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	82.1031	886	1479	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.0641	877	1479	95	below_threshold
Enterobacter cancerogenus	strain=FDAARGOS 1428	GCA_019047785.1	69218	69218	type	True	82.0089	873	1479	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_000213995.1	301105	158836	type	True	81.9817	875	1479	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	81.724	888	1479	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.6636	875	1479	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	81.6539	845	1479	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	81.5745	857	1479	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	81.4949	844	1479	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.4386	800	1479	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	81.4112	845	1479	95	below_threshold
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	81.406	855	1479	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	81.4048	858	1479	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	81.3679	855	1479	95	below_threshold
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	81.342	826	1479	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	81.2365	825	1479	95	below_threshold
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	81.1717	826	1479	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	81.1578	835	1479	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	81.0403	835	1479	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	81.0029	801	1479	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	80.9074	783	1479	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	80.8723	819	1479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:28,754] [INFO] DFAST Taxonomy check result was written to GCF_900450975.1_29859_B01_genomic.fna/tc_result.tsv
[2024-01-24 13:26:28,754] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:28,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:28,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/checkm_data
[2024-01-24 13:26:28,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:28,796] [INFO] Task started: CheckM
[2024-01-24 13:26:28,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900450975.1_29859_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900450975.1_29859_B01_genomic.fna/checkm_input GCF_900450975.1_29859_B01_genomic.fna/checkm_result
[2024-01-24 13:27:05,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:05,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:05,876] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:05,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:05,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900450975.1_29859_B01_genomic.fna/markers.fasta)
[2024-01-24 13:27:05,877] [INFO] Task started: Blastn
[2024-01-24 13:27:05,877] [INFO] Running command: blastn -query GCF_900450975.1_29859_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ce36c98-3ec4-4550-9aa2-3f8990cf44cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900450975.1_29859_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:07,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:07,007] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:07,007] [INFO] Target genome list was writen to GCF_900450975.1_29859_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:07,021] [INFO] Task started: fastANI
[2024-01-24 13:27:07,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgc516e376-722e-4e20-8257-f8be52bef313/GCF_900450975.1_29859_B01_genomic.fna.gz --refList GCF_900450975.1_29859_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900450975.1_29859_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:20,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:20,807] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:20,807] [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_000759795.1	s__Pseudescherichia vulneris	99.961	1425	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.06	96.32	0.93	0.89	6	conclusive
GCF_007680145.1	s__Pseudescherichia sp002298805	93.8771	1270	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.55	96.56	0.95	0.92	13	-
GCF_002918705.1	s__Pseudescherichia sp002918705	92.4131	1236	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.58	97.76	0.93	0.92	5	-
GCA_002480085.1	s__Pseudescherichia sp002480085	91.3358	1213	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116015.1	s__Enterobacter_D sp900116015	82.4187	954	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	97.94	97.83	0.93	0.90	7	-
GCF_004331265.1	s__Enterobacter wuhouensis	82.2198	885	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019047785.1	s__Enterobacter cancerogenus	82.0137	872	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	81.4978	834	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_006539725.1	s__Klebsiella terrigena	81.3148	830	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.25	96.63	0.88	0.85	68	-
GCA_016939855.1	s__Kluyvera ascorbata_C	81.2821	457	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814905.1	s__Kosakonia sp000814905	81.0795	833	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218705.1	s__Kluyvera sichuanensis	81.0691	832	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735365.1	s__Kluyvera ascorbata	80.9092	783	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCA_002377245.1	s__Phytobacter sp002377245	80.4343	659	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:20,809] [INFO] GTDB search result was written to GCF_900450975.1_29859_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:20,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:20,813] [INFO] DFAST_QC result json was written to GCF_900450975.1_29859_B01_genomic.fna/dqc_result.json
[2024-01-24 13:27:20,813] [INFO] DFAST_QC completed!
[2024-01-24 13:27:20,814] [INFO] Total running time: 0h1m33s