[2023-06-28 12:14:32,223] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:14:32,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:14:32,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference
[2023-06-28 12:14:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:14:34,557] [INFO] Task started: Prodigal
[2023-06-28 12:14:34,557] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1c4f7d5-b9c3-45a8-bd06-c0c3b0db8681/GCA_027484865.1_ASM2748486v1_genomic.fna.gz | prodigal -d GCA_027484865.1_ASM2748486v1_genomic.fna/cds.fna -a GCA_027484865.1_ASM2748486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:14:47,085] [INFO] Task succeeded: Prodigal
[2023-06-28 12:14:47,086] [INFO] Task started: HMMsearch
[2023-06-28 12:14:47,086] [INFO] Running command: hmmsearch --tblout GCA_027484865.1_ASM2748486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/reference_markers.hmm GCA_027484865.1_ASM2748486v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:14:47,404] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:14:47,406] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1c4f7d5-b9c3-45a8-bd06-c0c3b0db8681/GCA_027484865.1_ASM2748486v1_genomic.fna.gz]
[2023-06-28 12:14:47,446] [INFO] Query marker FASTA was written to GCA_027484865.1_ASM2748486v1_genomic.fna/markers.fasta
[2023-06-28 12:14:47,446] [INFO] Task started: Blastn
[2023-06-28 12:14:47,447] [INFO] Running command: blastn -query GCA_027484865.1_ASM2748486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/reference_markers.fasta -out GCA_027484865.1_ASM2748486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:14:48,323] [INFO] Task succeeded: Blastn
[2023-06-28 12:14:48,328] [INFO] Selected 19 target genomes.
[2023-06-28 12:14:48,329] [INFO] Target genome list was writen to GCA_027484865.1_ASM2748486v1_genomic.fna/target_genomes.txt
[2023-06-28 12:14:48,336] [INFO] Task started: fastANI
[2023-06-28 12:14:48,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1c4f7d5-b9c3-45a8-bd06-c0c3b0db8681/GCA_027484865.1_ASM2748486v1_genomic.fna.gz --refList GCA_027484865.1_ASM2748486v1_genomic.fna/target_genomes.txt --output GCA_027484865.1_ASM2748486v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:15:04,014] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:04,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:15:04,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:15:04,034] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 12:15:04,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 12:15:04,034] [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
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	98.8558	1192	1319	95	conclusive
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	84.2584	885	1319	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	81.4749	741	1319	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	81.45	744	1319	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	80.3078	698	1319	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.8491	557	1319	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.2623	522	1319	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.0063	506	1319	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.9096	544	1319	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.8307	509	1319	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.797	431	1319	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.7616	475	1319	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.7348	537	1319	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.715	511	1319	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	77.954	311	1319	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9495	411	1319	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	77.9345	313	1319	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9256	410	1319	95	below_threshold
Cypionkella psychrotolerans	strain=PAMC 27389	GCA_001294535.1	1678131	1678131	type	True	77.6563	398	1319	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:15:04,036] [INFO] DFAST Taxonomy check result was written to GCA_027484865.1_ASM2748486v1_genomic.fna/tc_result.tsv
[2023-06-28 12:15:04,038] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:15:04,039] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:15:04,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/checkm_data
[2023-06-28 12:15:04,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:15:04,090] [INFO] Task started: CheckM
[2023-06-28 12:15:04,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027484865.1_ASM2748486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027484865.1_ASM2748486v1_genomic.fna/checkm_input GCA_027484865.1_ASM2748486v1_genomic.fna/checkm_result
[2023-06-28 12:15:43,716] [INFO] Task succeeded: CheckM
[2023-06-28 12:15:43,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:15:43,741] [INFO] ===== Completeness check finished =====
[2023-06-28 12:15:43,742] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:15:43,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027484865.1_ASM2748486v1_genomic.fna/markers.fasta)
[2023-06-28 12:15:43,742] [INFO] Task started: Blastn
[2023-06-28 12:15:43,743] [INFO] Running command: blastn -query GCA_027484865.1_ASM2748486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9594df50-46fc-4b76-ae15-bd728df073fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027484865.1_ASM2748486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:15:45,229] [INFO] Task succeeded: Blastn
[2023-06-28 12:15:45,234] [INFO] Selected 16 target genomes.
[2023-06-28 12:15:45,235] [INFO] Target genome list was writen to GCA_027484865.1_ASM2748486v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:15:45,274] [INFO] Task started: fastANI
[2023-06-28 12:15:45,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1c4f7d5-b9c3-45a8-bd06-c0c3b0db8681/GCA_027484865.1_ASM2748486v1_genomic.fna.gz --refList GCA_027484865.1_ASM2748486v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027484865.1_ASM2748486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:15:59,285] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:59,307] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:15:59,308] [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_003060865.1	s__Gemmobacter_B sp003060865	98.8558	1192	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014243445.1	s__Gemmobacter_B straminiformis	84.2668	884	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	81.481	741	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	80.5496	724	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	80.4455	603	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	79.8159	594	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	79.7127	597	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCF_900110025.1	s__Gemmobacter aquatilis	79.2628	522	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	79.2372	445	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	79.007	506	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	78.9213	533	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	78.9008	546	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	78.8759	532	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	78.7582	435	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765775.1	s__Pseudorhodobacter sp016765775	78.5601	413	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.4492	328	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:15:59,311] [INFO] GTDB search result was written to GCA_027484865.1_ASM2748486v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:15:59,312] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:15:59,321] [INFO] DFAST_QC result json was written to GCA_027484865.1_ASM2748486v1_genomic.fna/dqc_result.json
[2023-06-28 12:15:59,321] [INFO] DFAST_QC completed!
[2023-06-28 12:15:59,322] [INFO] Total running time: 0h1m27s