[2024-01-25 19:38:35,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference
[2024-01-25 19:38:36,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,831] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg09097bcb-96e7-47bc-b8b7-c61e7f94469c/GCF_001521715.1_ASM152171v1_genomic.fna.gz | prodigal -d GCF_001521715.1_ASM152171v1_genomic.fna/cds.fna -a GCF_001521715.1_ASM152171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:48,262] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:48,263] [INFO] Task started: HMMsearch
[2024-01-25 19:38:48,263] [INFO] Running command: hmmsearch --tblout GCF_001521715.1_ASM152171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/reference_markers.hmm GCF_001521715.1_ASM152171v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:48,555] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:48,556] [INFO] Found 6/6 markers.
[2024-01-25 19:38:48,602] [INFO] Query marker FASTA was written to GCF_001521715.1_ASM152171v1_genomic.fna/markers.fasta
[2024-01-25 19:38:48,602] [INFO] Task started: Blastn
[2024-01-25 19:38:48,602] [INFO] Running command: blastn -query GCF_001521715.1_ASM152171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/reference_markers.fasta -out GCF_001521715.1_ASM152171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:49,425] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:49,428] [INFO] Selected 12 target genomes.
[2024-01-25 19:38:49,428] [INFO] Target genome list was writen to GCF_001521715.1_ASM152171v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:49,433] [INFO] Task started: fastANI
[2024-01-25 19:38:49,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg09097bcb-96e7-47bc-b8b7-c61e7f94469c/GCF_001521715.1_ASM152171v1_genomic.fna.gz --refList GCF_001521715.1_ASM152171v1_genomic.fna/target_genomes.txt --output GCF_001521715.1_ASM152171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:05,572] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:05,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:05,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:05,582] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:05,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:05,583] [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 asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	100.0	1599	1599	95	conclusive
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	99.9917	1583	1599	95	conclusive
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.3358	1325	1599	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	93.4093	1345	1599	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	93.3757	1318	1599	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	93.3486	1350	1599	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	93.3462	1262	1599	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.7221	1278	1599	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	91.0985	1281	1599	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.7014	1227	1599	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	89.0527	1265	1599	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.392	1226	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:05,584] [INFO] DFAST Taxonomy check result was written to GCF_001521715.1_ASM152171v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:05,584] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:05,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:05,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/checkm_data
[2024-01-25 19:39:05,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:05,637] [INFO] Task started: CheckM
[2024-01-25 19:39:05,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001521715.1_ASM152171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001521715.1_ASM152171v1_genomic.fna/checkm_input GCF_001521715.1_ASM152171v1_genomic.fna/checkm_result
[2024-01-25 19:39:40,374] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:40,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:40,397] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:40,397] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:40,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001521715.1_ASM152171v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:40,397] [INFO] Task started: Blastn
[2024-01-25 19:39:40,398] [INFO] Running command: blastn -query GCF_001521715.1_ASM152171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg328ea925-e544-475a-a68a-d23a449b9e24/dqc_reference/reference_markers_gtdb.fasta -out GCF_001521715.1_ASM152171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:41,564] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:41,567] [INFO] Selected 16 target genomes.
[2024-01-25 19:39:41,567] [INFO] Target genome list was writen to GCF_001521715.1_ASM152171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:41,587] [INFO] Task started: fastANI
[2024-01-25 19:39:41,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg09097bcb-96e7-47bc-b8b7-c61e7f94469c/GCF_001521715.1_ASM152171v1_genomic.fna.gz --refList GCF_001521715.1_ASM152171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001521715.1_ASM152171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:00,086] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:00,105] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:00,105] [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_001521715.1	s__Enterobacter asburiae	100.0	1599	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	conclusive
GCF_007035645.1	s__Enterobacter asburiae_B	96.8565	1361	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_002208095.1	s__Enterobacter cloacae_M	96.737	1372	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_008364625.1	s__Enterobacter dykesii	96.2074	1307	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_003634515.1	s__Enterobacter asburiae_A	96.0131	1337	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_000493015.1	s__Enterobacter sp000493015	95.4562	1346	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_008080435.1	s__Enterobacter asburiae_C	95.2168	1307	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_008364555.1	s__Enterobacter vonholyi	94.3358	1325	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001022965.1	s__Enterobacter cloacae_L	92.8984	1336	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.51	97.16	0.91	0.90	5	-
GCF_002939185.1	s__Enterobacter sichuanensis	91.7765	1260	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_001729765.1	s__Enterobacter kobei	91.092	1282	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_900322725.1	s__Enterobacter quasihormaechei	88.5439	1182	1599	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	88.3551	1239	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_000280495.2	s__Kosakonia radicincitans	81.8591	917	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:00,108] [INFO] GTDB search result was written to GCF_001521715.1_ASM152171v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:00,109] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:00,114] [INFO] DFAST_QC result json was written to GCF_001521715.1_ASM152171v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:00,114] [INFO] DFAST_QC completed!
[2024-01-25 19:40:00,114] [INFO] Total running time: 0h1m24s