[2024-01-24 11:59:12,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference
[2024-01-24 11:59:14,263] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,264] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,264] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4caf5c9-dd80-4f5d-a0af-372f3fe080b1/GCF_002943565.1_ASM294356v1_genomic.fna.gz | prodigal -d GCF_002943565.1_ASM294356v1_genomic.fna/cds.fna -a GCF_002943565.1_ASM294356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:28,089] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:28,089] [INFO] Task started: HMMsearch
[2024-01-24 11:59:28,089] [INFO] Running command: hmmsearch --tblout GCF_002943565.1_ASM294356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/reference_markers.hmm GCF_002943565.1_ASM294356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:28,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:28,386] [INFO] Found 6/6 markers.
[2024-01-24 11:59:28,428] [INFO] Query marker FASTA was written to GCF_002943565.1_ASM294356v1_genomic.fna/markers.fasta
[2024-01-24 11:59:28,429] [INFO] Task started: Blastn
[2024-01-24 11:59:28,429] [INFO] Running command: blastn -query GCF_002943565.1_ASM294356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/reference_markers.fasta -out GCF_002943565.1_ASM294356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:29,331] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:29,339] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:29,339] [INFO] Target genome list was writen to GCF_002943565.1_ASM294356v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:29,346] [INFO] Task started: fastANI
[2024-01-24 11:59:29,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4caf5c9-dd80-4f5d-a0af-372f3fe080b1/GCF_002943565.1_ASM294356v1_genomic.fna.gz --refList GCF_002943565.1_ASM294356v1_genomic.fna/target_genomes.txt --output GCF_002943565.1_ASM294356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:50,857] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:50,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:50,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:50,876] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:50,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:50,876] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	100.0	1633	1633	95	conclusive
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	77.7548	400	1633	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	77.6716	407	1633	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.258	201	1633	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.1946	194	1633	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.5719	126	1633	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.4283	173	1633	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	76.1891	143	1633	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	76.1844	111	1633	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	76.1021	164	1633	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	76.0653	150	1633	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	76.043	152	1633	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	76.0251	202	1633	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	76.0094	89	1633	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	75.9902	170	1633	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	75.9871	125	1633	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	75.9335	173	1633	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.814	166	1633	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	75.7617	164	1633	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.759	170	1633	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	75.7067	144	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:50,879] [INFO] DFAST Taxonomy check result was written to GCF_002943565.1_ASM294356v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:50,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:50,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:50,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/checkm_data
[2024-01-24 11:59:50,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:50,932] [INFO] Task started: CheckM
[2024-01-24 11:59:50,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002943565.1_ASM294356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002943565.1_ASM294356v1_genomic.fna/checkm_input GCF_002943565.1_ASM294356v1_genomic.fna/checkm_result
[2024-01-24 12:00:32,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:32,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:32,558] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:32,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:32,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002943565.1_ASM294356v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:32,559] [INFO] Task started: Blastn
[2024-01-24 12:00:32,559] [INFO] Running command: blastn -query GCF_002943565.1_ASM294356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97914d9e-03c3-4ab9-b83f-ea069903e7ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_002943565.1_ASM294356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:34,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:34,257] [INFO] Selected 12 target genomes.
[2024-01-24 12:00:34,257] [INFO] Target genome list was writen to GCF_002943565.1_ASM294356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:34,283] [INFO] Task started: fastANI
[2024-01-24 12:00:34,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4caf5c9-dd80-4f5d-a0af-372f3fe080b1/GCF_002943565.1_ASM294356v1_genomic.fna.gz --refList GCF_002943565.1_ASM294356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002943565.1_ASM294356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:43,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:43,346] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:43,346] [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_002943565.1	s__Marinicaulis flavus	100.0	1633	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002704915.1	s__Marinicaulis sp002704915	81.5222	811	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388885.1	s__Marinicaulis sp002388885	78.8085	444	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	78.4045	483	1633	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	77.78	396	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016125425.1	s__Amphiplicatus sp016125425	77.3027	303	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	77.268	288	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	77.0676	346	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.9245	182	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_003506635.1	s__CV81 sp003506635	76.8416	255	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696695.1	s__Terricaulis sp900696695	76.2302	165	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	99.53	99.53	0.91	0.91	2	-
GCA_016792765.1	s__SBBV01 sp016792765	75.4291	150	1633	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:43,348] [INFO] GTDB search result was written to GCF_002943565.1_ASM294356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:43,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:43,352] [INFO] DFAST_QC result json was written to GCF_002943565.1_ASM294356v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:43,352] [INFO] DFAST_QC completed!
[2024-01-24 12:00:43,353] [INFO] Total running time: 0h1m30s