[2024-01-24 14:23:05,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,235] [INFO] DQC Reference Directory: /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference
[2024-01-24 14:23:06,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,646] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,647] [INFO] Running command: gunzip -c /var/lib/cwl/stga5cf95c2-aadb-46cd-aebc-ee2948daf768/GCF_021469225.1_PDT001222236.1_genomic.fna.gz | prodigal -d GCF_021469225.1_PDT001222236.1_genomic.fna/cds.fna -a GCF_021469225.1_PDT001222236.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:21,743] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:21,743] [INFO] Task started: HMMsearch
[2024-01-24 14:23:21,743] [INFO] Running command: hmmsearch --tblout GCF_021469225.1_PDT001222236.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/reference_markers.hmm GCF_021469225.1_PDT001222236.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:22,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:22,116] [INFO] Found 6/6 markers.
[2024-01-24 14:23:22,168] [INFO] Query marker FASTA was written to GCF_021469225.1_PDT001222236.1_genomic.fna/markers.fasta
[2024-01-24 14:23:22,168] [INFO] Task started: Blastn
[2024-01-24 14:23:22,169] [INFO] Running command: blastn -query GCF_021469225.1_PDT001222236.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/reference_markers.fasta -out GCF_021469225.1_PDT001222236.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:23,144] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:23,148] [INFO] Selected 12 target genomes.
[2024-01-24 14:23:23,148] [INFO] Target genome list was writen to GCF_021469225.1_PDT001222236.1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:23,152] [INFO] Task started: fastANI
[2024-01-24 14:23:23,152] [INFO] Running command: fastANI --query /var/lib/cwl/stga5cf95c2-aadb-46cd-aebc-ee2948daf768/GCF_021469225.1_PDT001222236.1_genomic.fna.gz --refList GCF_021469225.1_PDT001222236.1_genomic.fna/target_genomes.txt --output GCF_021469225.1_PDT001222236.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:39,279] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:39,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:39,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:39,292] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:23:39,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:39,293] [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 cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	100.0	1788	1810	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_001997105.1	550	550	type	True	99.6895	1585	1810	95	conclusive
Enterobacter cloacae	strain=DSM 30054	GCA_013376815.1	550	550	type	True	99.5997	1624	1810	95	conclusive
Enterobacter cloacae	strain=FDAARGOS 1431	GCA_019047105.1	550	550	type	True	99.5928	1627	1810	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_000755525.1	550	550	type	True	99.5735	1627	1810	95	conclusive
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	89.2329	1322	1810	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	89.1233	1279	1810	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	87.8898	1288	1810	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.5729	1301	1810	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.0295	1054	1810	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	83.9226	1069	1810	95	below_threshold
Pantoea septica	strain=LMG 5345	GCA_002095575.1	472695	472695	type	True	78.7233	531	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:39,294] [INFO] DFAST Taxonomy check result was written to GCF_021469225.1_PDT001222236.1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:39,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:39,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:39,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/checkm_data
[2024-01-24 14:23:39,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:39,352] [INFO] Task started: CheckM
[2024-01-24 14:23:39,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021469225.1_PDT001222236.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021469225.1_PDT001222236.1_genomic.fna/checkm_input GCF_021469225.1_PDT001222236.1_genomic.fna/checkm_result
[2024-01-24 14:24:25,793] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:25,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:25,816] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:25,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:25,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021469225.1_PDT001222236.1_genomic.fna/markers.fasta)
[2024-01-24 14:24:25,817] [INFO] Task started: Blastn
[2024-01-24 14:24:25,817] [INFO] Running command: blastn -query GCF_021469225.1_PDT001222236.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9bd59e7-f348-43c1-8422-5850cc9fa8df/dqc_reference/reference_markers_gtdb.fasta -out GCF_021469225.1_PDT001222236.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:27,033] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:27,037] [INFO] Selected 25 target genomes.
[2024-01-24 14:24:27,037] [INFO] Target genome list was writen to GCF_021469225.1_PDT001222236.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:27,056] [INFO] Task started: fastANI
[2024-01-24 14:24:27,056] [INFO] Running command: fastANI --query /var/lib/cwl/stga5cf95c2-aadb-46cd-aebc-ee2948daf768/GCF_021469225.1_PDT001222236.1_genomic.fna.gz --refList GCF_021469225.1_PDT001222236.1_genomic.fna/target_genomes_gtdb.txt --output GCF_021469225.1_PDT001222236.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:54,489] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:54,511] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:54,511] [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_000025565.1	s__Enterobacter cloacae	99.5746	1625	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	conclusive
GCF_002939185.1	s__Enterobacter sichuanensis	89.2794	1291	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_003634515.1	s__Enterobacter asburiae_A	89.0159	1316	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_001521715.1	s__Enterobacter asburiae	89.0088	1269	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_007035645.1	s__Enterobacter asburiae_B	88.975	1302	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001729805.1	s__Enterobacter roggenkampii	88.9581	1297	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_009755685.1	s__Enterobacter sp000568095	88.9534	1294	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_008080435.1	s__Enterobacter asburiae_C	88.8733	1321	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_008364625.1	s__Enterobacter dykesii	88.8397	1272	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_900324475.1	s__Enterobacter bugandensis	88.7175	1318	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_011754535.1	s__Enterobacter cloacae_N	88.7088	1326	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_001984825.2	s__Enterobacter chengduensis	88.7078	1331	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_003046225.1	s__Enterobacter cloacae_I	88.6969	1310	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.61	95.47	0.89	0.86	14	-
GCF_008364555.1	s__Enterobacter vonholyi	88.6687	1282	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001729765.1	s__Enterobacter kobei	88.4864	1312	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_001750725.1	s__Enterobacter ludwigii	88.2533	1354	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.79	98.47	0.93	0.83	88	-
GCF_014169315.1	s__Enterobacter cloacae_P	88.1004	1230	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.13	99.10	0.85	0.85	3	-
GCF_900322725.1	s__Enterobacter quasihormaechei	87.9046	1332	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_019047785.1	s__Enterobacter cancerogenus	86.7513	1242	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
GCF_011290365.1	s__Leclercia sp003024485	84.3672	1132	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCF_017348915.1	s__UBA7405 sp000755535	83.9288	1066	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.3106	926	1810	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_014168815.1	s__Kluyvera ascorbata_B	82.1432	922	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCF_000734965.1	s__Trabulsiella guamensis	81.4012	854	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801695.1	s__Pantoea stewartii	79.3594	412	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.82	98.55	0.82	0.77	34	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:54,513] [INFO] GTDB search result was written to GCF_021469225.1_PDT001222236.1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:54,514] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:54,518] [INFO] DFAST_QC result json was written to GCF_021469225.1_PDT001222236.1_genomic.fna/dqc_result.json
[2024-01-24 14:24:54,518] [INFO] DFAST_QC completed!
[2024-01-24 14:24:54,518] [INFO] Total running time: 0h1m49s