[2024-01-24 11:34:40,907] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference
[2024-01-24 11:34:42,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,316] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,316] [INFO] Running command: gunzip -c /var/lib/cwl/stgdeacc158-652a-4abf-a59b-c0abce8d1d1d/GCF_001484765.1_ASM148476v1_genomic.fna.gz | prodigal -d GCF_001484765.1_ASM148476v1_genomic.fna/cds.fna -a GCF_001484765.1_ASM148476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:56,587] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:56,588] [INFO] Task started: HMMsearch
[2024-01-24 11:34:56,588] [INFO] Running command: hmmsearch --tblout GCF_001484765.1_ASM148476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/reference_markers.hmm GCF_001484765.1_ASM148476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:56,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:56,936] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,006] [INFO] Query marker FASTA was written to GCF_001484765.1_ASM148476v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,007] [INFO] Task started: Blastn
[2024-01-24 11:34:57,007] [INFO] Running command: blastn -query GCF_001484765.1_ASM148476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/reference_markers.fasta -out GCF_001484765.1_ASM148476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:57,898] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:57,902] [INFO] Selected 32 target genomes.
[2024-01-24 11:34:57,902] [INFO] Target genome list was writen to GCF_001484765.1_ASM148476v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:57,928] [INFO] Task started: fastANI
[2024-01-24 11:34:57,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeacc158-652a-4abf-a59b-c0abce8d1d1d/GCF_001484765.1_ASM148476v1_genomic.fna.gz --refList GCF_001484765.1_ASM148476v1_genomic.fna/target_genomes.txt --output GCF_001484765.1_ASM148476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:26,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:26,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:26,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:26,809] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:26,809] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:26,809] [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
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	80.3146	731	1775	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	80.3032	736	1775	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	80.255	735	1775	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	80.2437	737	1775	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	80.2097	666	1775	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.0633	690	1775	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	80.0542	743	1775	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	79.9599	656	1775	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	79.9547	691	1775	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	79.9422	773	1775	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	79.9348	738	1775	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	79.9342	674	1775	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	79.917	668	1775	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	79.9119	685	1775	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	79.9059	715	1775	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	79.9024	712	1775	95	below_threshold
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	79.8921	680	1775	95	below_threshold
Cronobacter sakazakii	strain=NBRC 102416	GCA_000684935.1	28141	28141	type	True	79.8917	677	1775	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	79.8824	676	1775	95	below_threshold
Klebsiella pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	79.8751	721	1775	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	79.8425	684	1775	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	79.8266	692	1775	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	79.6951	627	1775	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	79.6272	658	1775	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	79.6069	642	1775	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	79.6047	671	1775	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	79.5699	646	1775	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	79.5575	555	1775	95	below_threshold
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	79.5566	639	1775	95	below_threshold
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	79.5071	629	1775	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	79.4836	606	1775	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	79.4656	593	1775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:26,811] [INFO] DFAST Taxonomy check result was written to GCF_001484765.1_ASM148476v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:26,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:26,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:26,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/checkm_data
[2024-01-24 11:35:26,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:26,862] [INFO] Task started: CheckM
[2024-01-24 11:35:26,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001484765.1_ASM148476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001484765.1_ASM148476v1_genomic.fna/checkm_input GCF_001484765.1_ASM148476v1_genomic.fna/checkm_result
[2024-01-24 11:36:08,382] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:08,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:08,403] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:08,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:08,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001484765.1_ASM148476v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:08,404] [INFO] Task started: Blastn
[2024-01-24 11:36:08,405] [INFO] Running command: blastn -query GCF_001484765.1_ASM148476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8699df2-e879-4b76-8046-d35464966a8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001484765.1_ASM148476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:09,506] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:09,509] [INFO] Selected 25 target genomes.
[2024-01-24 11:36:09,509] [INFO] Target genome list was writen to GCF_001484765.1_ASM148476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:09,525] [INFO] Task started: fastANI
[2024-01-24 11:36:09,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeacc158-652a-4abf-a59b-c0abce8d1d1d/GCF_001484765.1_ASM148476v1_genomic.fna.gz --refList GCF_001484765.1_ASM148476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001484765.1_ASM148476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:32,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:32,279] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:32,280] [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
GCA_001484765.1	s__Erwinia_A teleogrylli	100.0	1772	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000751755.1	s__Klebsiella quasipneumoniae	80.2748	733	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	80.1533	709	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_009907385.1	s__Atlantibacter hermannii_A	80.1412	712	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001888805.2	s__Enterobacter_D sp001888805	80.0712	668	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	97.70	97.19	0.94	0.94	3	-
GCF_007570865.1	s__Atlantibacter subterranea	80.0027	714	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCA_000027065.2	s__Cronobacter turicensis	79.9558	684	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277215.2	s__Cronobacter malonaticus	79.9447	672	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_900200035.1	s__Klebsiella grimontii	79.9371	773	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_000742135.1	s__Klebsiella pneumoniae	79.9099	713	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_000696575.1	s__Siccibacter colletis	79.9025	648	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237635.1	s__Enterobacter_B sp019237635	79.883	639	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277195.1	s__Cronobacter muytjensii	79.8822	674	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_900978845.1	s__Klebsiella africana	79.8737	681	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000321045.1	s__Phytobacter massiliensis	79.7578	683	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001297775.1	s__Trabulsiella odontotermitis	79.6858	675	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	99.98	99.97	0.99	0.99	5	-
GCF_001654985.1	s__Kluyvera georgiana	79.6159	640	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.06	98.06	0.84	0.84	2	-
GCF_000759835.1	s__Citrobacter_A sedlakii	79.6122	682	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCA_002211745.1	s__Kluyvera georgiana_A	79.6086	647	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	79.5736	648	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCF_003628475.1	s__Buttiauxella sp002321695	79.546	607	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.11	99.11	0.94	0.94	2	-
GCF_001598695.1	s__Klebsiella oxytoca	79.5394	749	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_000735455.1	s__Yokenella regensburgei	79.5066	630	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yokenella	95.0	99.37	98.92	0.95	0.91	10	-
GCF_000155975.1	s__Citrobacter portucalensis_A	79.4288	643	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001266615.1	s__Kluyvera cryocrescens_A	78.9778	579	1775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:32,281] [INFO] GTDB search result was written to GCF_001484765.1_ASM148476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:32,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:32,287] [INFO] DFAST_QC result json was written to GCF_001484765.1_ASM148476v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:32,287] [INFO] DFAST_QC completed!
[2024-01-24 11:36:32,287] [INFO] Total running time: 0h1m51s