[2023-06-18 21:38:40,901] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:38:40,906] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:38:40,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference
[2023-06-18 21:38:42,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:38:42,725] [INFO] Task started: Prodigal
[2023-06-18 21:38:42,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07b4004-723c-4c86-8476-09362e9a7258/GCA_018376065.1_ASM1837606v1_genomic.fna.gz | prodigal -d GCA_018376065.1_ASM1837606v1_genomic.fna/cds.fna -a GCA_018376065.1_ASM1837606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:38:54,808] [INFO] Task succeeded: Prodigal
[2023-06-18 21:38:54,809] [INFO] Task started: HMMsearch
[2023-06-18 21:38:54,809] [INFO] Running command: hmmsearch --tblout GCA_018376065.1_ASM1837606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/reference_markers.hmm GCA_018376065.1_ASM1837606v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:38:55,090] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:38:55,091] [INFO] Found 6/6 markers.
[2023-06-18 21:38:55,135] [INFO] Query marker FASTA was written to GCA_018376065.1_ASM1837606v1_genomic.fna/markers.fasta
[2023-06-18 21:38:55,136] [INFO] Task started: Blastn
[2023-06-18 21:38:55,136] [INFO] Running command: blastn -query GCA_018376065.1_ASM1837606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/reference_markers.fasta -out GCA_018376065.1_ASM1837606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:38:55,967] [INFO] Task succeeded: Blastn
[2023-06-18 21:38:55,974] [INFO] Selected 12 target genomes.
[2023-06-18 21:38:55,974] [INFO] Target genome list was writen to GCA_018376065.1_ASM1837606v1_genomic.fna/target_genomes.txt
[2023-06-18 21:38:55,981] [INFO] Task started: fastANI
[2023-06-18 21:38:55,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07b4004-723c-4c86-8476-09362e9a7258/GCA_018376065.1_ASM1837606v1_genomic.fna.gz --refList GCA_018376065.1_ASM1837606v1_genomic.fna/target_genomes.txt --output GCA_018376065.1_ASM1837606v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:09,794] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:09,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:09,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:09,805] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-06-18 21:39:09,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 21:39:09,805] [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	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	98.5701	1384	1487	95	conclusive
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_000213995.1	301105	158836	type	True	98.5454	1381	1487	95	conclusive
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	98.5256	1388	1487	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	94.9931	1312	1487	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	94.9717	1311	1487	95	below_threshold
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	94.9619	1301	1487	95	below_threshold
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	94.7497	1301	1487	95	below_threshold
Enterobacter hormaechei subsp. hoffmannii	strain=DSM 14563	GCA_001729745.1	1812934	158836	type	True	94.3099	1299	1487	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	88.1129	1153	1487	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.0576	1202	1487	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	87.5234	1171	1487	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	87.3178	1222	1487	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:39:09,808] [INFO] DFAST Taxonomy check result was written to GCA_018376065.1_ASM1837606v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:09,808] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:09,808] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:09,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/checkm_data
[2023-06-18 21:39:09,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:09,855] [INFO] Task started: CheckM
[2023-06-18 21:39:09,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376065.1_ASM1837606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376065.1_ASM1837606v1_genomic.fna/checkm_input GCA_018376065.1_ASM1837606v1_genomic.fna/checkm_result
[2023-06-18 21:39:49,000] [INFO] Task succeeded: CheckM
[2023-06-18 21:39:49,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:39:49,034] [INFO] ===== Completeness check finished =====
[2023-06-18 21:39:49,035] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:39:49,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376065.1_ASM1837606v1_genomic.fna/markers.fasta)
[2023-06-18 21:39:49,036] [INFO] Task started: Blastn
[2023-06-18 21:39:49,036] [INFO] Running command: blastn -query GCA_018376065.1_ASM1837606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4e32a9-f1ad-493e-90cc-062db12ff97d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376065.1_ASM1837606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:50,153] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:50,160] [INFO] Selected 10 target genomes.
[2023-06-18 21:39:50,160] [INFO] Target genome list was writen to GCA_018376065.1_ASM1837606v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:39:50,193] [INFO] Task started: fastANI
[2023-06-18 21:39:50,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07b4004-723c-4c86-8476-09362e9a7258/GCA_018376065.1_ASM1837606v1_genomic.fna.gz --refList GCA_018376065.1_ASM1837606v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376065.1_ASM1837606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:40:01,743] [INFO] Task succeeded: fastANI
[2023-06-18 21:40:01,754] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:40:01,754] [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_001875655.1	s__Enterobacter hormaechei	98.5256	1388	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	conclusive
GCF_011078175.1	s__Enterobacter cloacae_Q	94.4606	1276	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001729745.1	s__Enterobacter hormaechei_A	94.3099	1299	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_900322725.1	s__Enterobacter quasihormaechei	93.0455	1281	1487	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	90.9859	1278	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_900324475.1	s__Enterobacter bugandensis	88.8266	1200	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_002208095.1	s__Enterobacter cloacae_M	87.8534	1209	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_001729765.1	s__Enterobacter kobei	87.6255	1197	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_014490785.1	s__Kosakonia sp014490785	81.0356	820	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010231475.1	s__Citrobacter sp010231475	81.0226	768	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:40:01,756] [INFO] GTDB search result was written to GCA_018376065.1_ASM1837606v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:40:01,757] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:40:01,761] [INFO] DFAST_QC result json was written to GCA_018376065.1_ASM1837606v1_genomic.fna/dqc_result.json
[2023-06-18 21:40:01,761] [INFO] DFAST_QC completed!
[2023-06-18 21:40:01,761] [INFO] Total running time: 0h1m21s