[2024-01-24 14:12:47,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,286] [INFO] DQC Reference Directory: /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference
[2024-01-24 14:12:48,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,538] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,538] [INFO] Running command: gunzip -c /var/lib/cwl/stga2592693-da75-47ca-b37c-f006f17b53a9/GCF_003399445.1_ASM339944v1_genomic.fna.gz | prodigal -d GCF_003399445.1_ASM339944v1_genomic.fna/cds.fna -a GCF_003399445.1_ASM339944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:58,469] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:58,470] [INFO] Task started: HMMsearch
[2024-01-24 14:12:58,470] [INFO] Running command: hmmsearch --tblout GCF_003399445.1_ASM339944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/reference_markers.hmm GCF_003399445.1_ASM339944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:58,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:58,718] [INFO] Found 6/6 markers.
[2024-01-24 14:12:58,750] [INFO] Query marker FASTA was written to GCF_003399445.1_ASM339944v1_genomic.fna/markers.fasta
[2024-01-24 14:12:58,750] [INFO] Task started: Blastn
[2024-01-24 14:12:58,750] [INFO] Running command: blastn -query GCF_003399445.1_ASM339944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/reference_markers.fasta -out GCF_003399445.1_ASM339944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:59,611] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:59,615] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:59,616] [INFO] Target genome list was writen to GCF_003399445.1_ASM339944v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:59,626] [INFO] Task started: fastANI
[2024-01-24 14:12:59,626] [INFO] Running command: fastANI --query /var/lib/cwl/stga2592693-da75-47ca-b37c-f006f17b53a9/GCF_003399445.1_ASM339944v1_genomic.fna.gz --refList GCF_003399445.1_ASM339944v1_genomic.fna/target_genomes.txt --output GCF_003399445.1_ASM339944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:11,664] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:11,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:11,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:11,689] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:11,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:11,690] [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
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	100.0	1125	1125	95	conclusive
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	77.5886	152	1125	95	below_threshold
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	77.2281	138	1125	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	77.2017	205	1125	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	77.0561	170	1125	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	77.0258	172	1125	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.0257	176	1125	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.0156	181	1125	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.8457	149	1125	95	below_threshold
Parvularcula bermudensis	strain=HTCC2503	GCA_000152825.2	208216	208216	type	True	76.793	123	1125	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.2435	104	1125	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.2127	55	1125	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	76.1184	52	1125	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	75.757	61	1125	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	75.6131	59	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:11,691] [INFO] DFAST Taxonomy check result was written to GCF_003399445.1_ASM339944v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:11,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:11,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:11,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/checkm_data
[2024-01-24 14:13:11,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:11,731] [INFO] Task started: CheckM
[2024-01-24 14:13:11,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003399445.1_ASM339944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003399445.1_ASM339944v1_genomic.fna/checkm_input GCF_003399445.1_ASM339944v1_genomic.fna/checkm_result
[2024-01-24 14:13:45,841] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:45,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:45,860] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:45,860] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:45,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003399445.1_ASM339944v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:45,861] [INFO] Task started: Blastn
[2024-01-24 14:13:45,862] [INFO] Running command: blastn -query GCF_003399445.1_ASM339944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde96ecba-51ca-4d8c-8924-a193052aeb82/dqc_reference/reference_markers_gtdb.fasta -out GCF_003399445.1_ASM339944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:47,453] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:47,456] [INFO] Selected 18 target genomes.
[2024-01-24 14:13:47,456] [INFO] Target genome list was writen to GCF_003399445.1_ASM339944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:47,485] [INFO] Task started: fastANI
[2024-01-24 14:13:47,485] [INFO] Running command: fastANI --query /var/lib/cwl/stga2592693-da75-47ca-b37c-f006f17b53a9/GCF_003399445.1_ASM339944v1_genomic.fna.gz --refList GCF_003399445.1_ASM339944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003399445.1_ASM339944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:58,871] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:58,889] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:58,889] [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_003399445.1	s__Parvularcula sp003399445	100.0	1125	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013085255.1	s__Parvularcula mediterranea	77.6075	151	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651915.1	s__Parvularcula lutaonensis	77.2281	138	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	77.2017	205	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	77.0707	169	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640095.1	s__Aquisalinus flavus	77.0013	182	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199615.1	s__Parvularcula dongshanensis	76.8457	149	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152825.2	s__Parvularcula bermudensis	76.793	123	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	76.6452	102	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.5722	82	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	76.4431	128	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	76.4009	103	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002704915.1	s__Marinicaulis sp002704915	76.2097	121	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019145.1	s__Caulobacter sp000019145	75.9052	59	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	75.8506	94	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977555.1	s__Caulobacter rhizosphaerae	75.7773	60	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	-
GCF_001426905.1	s__Caulobacter sp001426905	75.5997	57	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.12	99.12	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:58,891] [INFO] GTDB search result was written to GCF_003399445.1_ASM339944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:58,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:58,896] [INFO] DFAST_QC result json was written to GCF_003399445.1_ASM339944v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:58,896] [INFO] DFAST_QC completed!
[2024-01-24 14:13:58,896] [INFO] Total running time: 0h1m12s