[2023-06-27 13:28:57,616] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:28:57,634] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:28:57,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference
[2023-06-27 13:29:00,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:29:00,346] [INFO] Task started: Prodigal
[2023-06-27 13:29:00,347] [INFO] Running command: gunzip -c /var/lib/cwl/stgd76c30c6-f594-4a8b-ac13-9d54680b040f/GCA_002415285.1_ASM241528v1_genomic.fna.gz | prodigal -d GCA_002415285.1_ASM241528v1_genomic.fna/cds.fna -a GCA_002415285.1_ASM241528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:29:12,695] [INFO] Task succeeded: Prodigal
[2023-06-27 13:29:12,696] [INFO] Task started: HMMsearch
[2023-06-27 13:29:12,696] [INFO] Running command: hmmsearch --tblout GCA_002415285.1_ASM241528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/reference_markers.hmm GCA_002415285.1_ASM241528v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:29:12,977] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:29:12,979] [INFO] Found 6/6 markers.
[2023-06-27 13:29:13,020] [INFO] Query marker FASTA was written to GCA_002415285.1_ASM241528v1_genomic.fna/markers.fasta
[2023-06-27 13:29:13,020] [INFO] Task started: Blastn
[2023-06-27 13:29:13,020] [INFO] Running command: blastn -query GCA_002415285.1_ASM241528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/reference_markers.fasta -out GCA_002415285.1_ASM241528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:13,955] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:13,959] [INFO] Selected 32 target genomes.
[2023-06-27 13:29:13,960] [INFO] Target genome list was writen to GCA_002415285.1_ASM241528v1_genomic.fna/target_genomes.txt
[2023-06-27 13:29:13,973] [INFO] Task started: fastANI
[2023-06-27 13:29:13,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgd76c30c6-f594-4a8b-ac13-9d54680b040f/GCA_002415285.1_ASM241528v1_genomic.fna.gz --refList GCA_002415285.1_ASM241528v1_genomic.fna/target_genomes.txt --output GCA_002415285.1_ASM241528v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:29:44,340] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:44,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:29:44,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:29:44,365] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:29:44,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 13:29:44,366] [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	82.3644	937	1492	95	below_threshold
Pseudescherichia vulneris	strain=NBRC 102420	GCA_000759795.1	566	566	type	True	82.3357	928	1492	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.9326	914	1492	95	below_threshold
Leclercia adecarboxylata	strain=NBRC 102595	GCA_001515505.1	83655	83655	suspected-type	True	81.9025	929	1492	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.8489	863	1492	95	below_threshold
Leclercia adecarboxylata	strain=ATCC 23216	GCA_000735515.1	83655	83655	suspected-type	True	81.8204	932	1492	95	below_threshold
Leclercia adecarboxylata	strain=FDAARGOS_1505	GCA_020097395.1	83655	83655	suspected-type	True	81.8183	953	1492	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	81.7882	894	1492	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7569	929	1492	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7182	876	1492	95	below_threshold
Lelliottia aquatilis	strain=6331-17	GCA_002923025.1	2080838	2080838	type	True	81.6945	940	1492	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	81.5817	922	1492	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	81.5799	908	1492	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.415	884	1492	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	81.3067	809	1492	95	below_threshold
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	81.2724	833	1492	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	81.2242	864	1492	95	below_threshold
Citrobacter amalonaticus	strain=JCM 1661	GCA_018323885.1	35703	35703	type	True	81.2229	843	1492	95	below_threshold
Klebsiella pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	80.9806	784	1492	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.9695	839	1492	95	below_threshold
Raoultella electrica	strain=DSM 102253	GCA_006711645.1	1259973	1259973	type	True	80.9691	771	1492	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	80.9567	775	1492	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	80.9053	799	1492	95	below_threshold
Raoultella ornithinolytica	strain=NBRC 105727	GCA_001598295.1	54291	54291	type	True	80.8841	782	1492	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	80.8684	810	1492	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	80.8248	731	1492	95	below_threshold
Escherichia fergusonii	strain=ATCC 35469T	GCA_000026225.1	564	564	type	True	80.8149	687	1492	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	80.8055	742	1492	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	80.7935	714	1492	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	80.7691	694	1492	95	below_threshold
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	80.4764	744	1492	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	80.4713	758	1492	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:29:44,368] [INFO] DFAST Taxonomy check result was written to GCA_002415285.1_ASM241528v1_genomic.fna/tc_result.tsv
[2023-06-27 13:29:44,368] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:29:44,369] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:29:44,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/checkm_data
[2023-06-27 13:29:44,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:29:44,418] [INFO] Task started: CheckM
[2023-06-27 13:29:44,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002415285.1_ASM241528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002415285.1_ASM241528v1_genomic.fna/checkm_input GCA_002415285.1_ASM241528v1_genomic.fna/checkm_result
[2023-06-27 13:30:24,003] [INFO] Task succeeded: CheckM
[2023-06-27 13:30:24,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:30:24,030] [INFO] ===== Completeness check finished =====
[2023-06-27 13:30:24,030] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:30:24,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002415285.1_ASM241528v1_genomic.fna/markers.fasta)
[2023-06-27 13:30:24,031] [INFO] Task started: Blastn
[2023-06-27 13:30:24,031] [INFO] Running command: blastn -query GCA_002415285.1_ASM241528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c6dcbfb-d913-4a2e-89e2-36cec6f3ddb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_002415285.1_ASM241528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:30:25,474] [INFO] Task succeeded: Blastn
[2023-06-27 13:30:25,478] [INFO] Selected 14 target genomes.
[2023-06-27 13:30:25,478] [INFO] Target genome list was writen to GCA_002415285.1_ASM241528v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:30:25,495] [INFO] Task started: fastANI
[2023-06-27 13:30:25,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgd76c30c6-f594-4a8b-ac13-9d54680b040f/GCA_002415285.1_ASM241528v1_genomic.fna.gz --refList GCA_002415285.1_ASM241528v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002415285.1_ASM241528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:30:40,528] [INFO] Task succeeded: fastANI
[2023-06-27 13:30:40,554] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:30:40,555] [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_900116015.1	s__Enterobacter_D sp900116015	97.9669	1392	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	97.94	97.83	0.93	0.90	7	conclusive
GCF_001888805.2	s__Enterobacter_D sp001888805	84.3792	1117	1492	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_018323985.1	s__Enterobacter_D kobei_A	84.2829	1122	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	99.37	98.44	0.98	0.93	6	-
GCA_019218745.1	s__Enterobacter_D sp019218745	84.1983	1088	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002918705.1	s__Pseudescherichia sp002918705	82.2142	954	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.58	97.76	0.93	0.92	5	-
GCF_007680145.1	s__Pseudescherichia sp002298805	82.1107	951	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.55	96.56	0.95	0.92	13	-
GCF_007035645.1	s__Enterobacter asburiae_B	81.8152	916	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_000321045.1	s__Phytobacter massiliensis	81.4339	923	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015234305.1	s__Superficieibacter sp900766525	81.3187	889	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	96.26	96.26	0.86	0.86	2	-
GCF_014218705.1	s__Kluyvera sichuanensis	81.3117	808	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018252635.1	s__Citrobacter_A amalonaticus_E	81.1836	821	1492	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_009907385.1	s__Atlantibacter hermannii_A	81.0264	822	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026225.1	s__Escherichia fergusonii	80.8147	687	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_003697165.2	s__Escherichia coli	80.8105	741	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
--------------------------------------------------------------------------------
[2023-06-27 13:30:40,558] [INFO] GTDB search result was written to GCA_002415285.1_ASM241528v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:30:40,559] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:30:40,564] [INFO] DFAST_QC result json was written to GCA_002415285.1_ASM241528v1_genomic.fna/dqc_result.json
[2023-06-27 13:30:40,565] [INFO] DFAST_QC completed!
[2023-06-27 13:30:40,565] [INFO] Total running time: 0h1m43s