[2024-01-25 17:52:35,368] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:35,369] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:35,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference
[2024-01-25 17:52:36,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:36,507] [INFO] Task started: Prodigal
[2024-01-25 17:52:36,507] [INFO] Running command: gunzip -c /var/lib/cwl/stga9e212ff-a714-4231-b181-1ed84f3172f1/GCF_024505085.1_ASM2450508v1_genomic.fna.gz | prodigal -d GCF_024505085.1_ASM2450508v1_genomic.fna/cds.fna -a GCF_024505085.1_ASM2450508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:43,985] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:43,985] [INFO] Task started: HMMsearch
[2024-01-25 17:52:43,986] [INFO] Running command: hmmsearch --tblout GCF_024505085.1_ASM2450508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/reference_markers.hmm GCF_024505085.1_ASM2450508v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:44,183] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:44,184] [INFO] Found 6/6 markers.
[2024-01-25 17:52:44,210] [INFO] Query marker FASTA was written to GCF_024505085.1_ASM2450508v1_genomic.fna/markers.fasta
[2024-01-25 17:52:44,210] [INFO] Task started: Blastn
[2024-01-25 17:52:44,211] [INFO] Running command: blastn -query GCF_024505085.1_ASM2450508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/reference_markers.fasta -out GCF_024505085.1_ASM2450508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:45,049] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:45,052] [INFO] Selected 18 target genomes.
[2024-01-25 17:52:45,052] [INFO] Target genome list was writen to GCF_024505085.1_ASM2450508v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:45,064] [INFO] Task started: fastANI
[2024-01-25 17:52:45,064] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e212ff-a714-4231-b181-1ed84f3172f1/GCF_024505085.1_ASM2450508v1_genomic.fna.gz --refList GCF_024505085.1_ASM2450508v1_genomic.fna/target_genomes.txt --output GCF_024505085.1_ASM2450508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:58,707] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:58,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:58,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:58,718] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:58,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:58,719] [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 mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	78.9148	468	1040	95	below_threshold
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	78.8099	440	1040	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	78.1822	314	1040	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	77.8664	308	1040	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.1784	157	1040	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.146	153	1040	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.8	130	1040	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.7131	165	1040	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	76.704	91	1040	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.6333	105	1040	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.1682	120	1040	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.1436	125	1040	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	76.1083	51	1040	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	76.0921	114	1040	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.9841	133	1040	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.9798	151	1040	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.9122	101	1040	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	75.9005	91	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:58,720] [INFO] DFAST Taxonomy check result was written to GCF_024505085.1_ASM2450508v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:58,721] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:58,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:58,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/checkm_data
[2024-01-25 17:52:58,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:58,755] [INFO] Task started: CheckM
[2024-01-25 17:52:58,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024505085.1_ASM2450508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024505085.1_ASM2450508v1_genomic.fna/checkm_input GCF_024505085.1_ASM2450508v1_genomic.fna/checkm_result
[2024-01-25 17:53:23,494] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:23,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:23,512] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:23,512] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:23,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024505085.1_ASM2450508v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:23,513] [INFO] Task started: Blastn
[2024-01-25 17:53:23,513] [INFO] Running command: blastn -query GCF_024505085.1_ASM2450508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28bce27a-155d-4e74-96f7-57e60a423e16/dqc_reference/reference_markers_gtdb.fasta -out GCF_024505085.1_ASM2450508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:25,194] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:25,197] [INFO] Selected 16 target genomes.
[2024-01-25 17:53:25,198] [INFO] Target genome list was writen to GCF_024505085.1_ASM2450508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:25,215] [INFO] Task started: fastANI
[2024-01-25 17:53:25,215] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e212ff-a714-4231-b181-1ed84f3172f1/GCF_024505085.1_ASM2450508v1_genomic.fna.gz --refList GCF_024505085.1_ASM2450508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024505085.1_ASM2450508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:35,579] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:35,589] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:53:35,589] [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_013085255.1	s__Parvularcula mediterranea	78.9245	467	1040	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	78.8062	441	1040	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	78.17	315	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	77.8781	307	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	77.196	156	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013215175.1	s__Parvularcula sp013215175	77.0438	204	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122085.1	s__WD6-1 sp003122085	76.8569	123	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	76.8	130	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	76.4242	93	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281955.1	s__Caulobacter sp000281955	76.3312	135	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182275.1	s__Hoeflea marina	76.1621	107	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	76.1274	99	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216735.1	s__Bradyrhizobium sp004216735	76.0376	129	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.9263	152	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009694215.1	s__Z2-YC6860 sp009694215	75.8278	65	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697125.1	s__J013 sp003697125	75.7271	91	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__J013	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:35,590] [INFO] GTDB search result was written to GCF_024505085.1_ASM2450508v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:35,591] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:35,594] [INFO] DFAST_QC result json was written to GCF_024505085.1_ASM2450508v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:35,594] [INFO] DFAST_QC completed!
[2024-01-25 17:53:35,594] [INFO] Total running time: 0h1m0s