[2024-01-24 13:31:12,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,173] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference
[2024-01-24 13:31:13,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,400] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg11f368d6-a986-4a93-84b0-7c92f193c873/GCF_003591515.1_ASM359151v1_genomic.fna.gz | prodigal -d GCF_003591515.1_ASM359151v1_genomic.fna/cds.fna -a GCF_003591515.1_ASM359151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:27,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:27,361] [INFO] Task started: HMMsearch
[2024-01-24 13:31:27,361] [INFO] Running command: hmmsearch --tblout GCF_003591515.1_ASM359151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/reference_markers.hmm GCF_003591515.1_ASM359151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:27,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:27,588] [INFO] Found 6/6 markers.
[2024-01-24 13:31:27,628] [INFO] Query marker FASTA was written to GCF_003591515.1_ASM359151v1_genomic.fna/markers.fasta
[2024-01-24 13:31:27,629] [INFO] Task started: Blastn
[2024-01-24 13:31:27,629] [INFO] Running command: blastn -query GCF_003591515.1_ASM359151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/reference_markers.fasta -out GCF_003591515.1_ASM359151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:28,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:28,434] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:28,435] [INFO] Target genome list was writen to GCF_003591515.1_ASM359151v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:28,447] [INFO] Task started: fastANI
[2024-01-24 13:31:28,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg11f368d6-a986-4a93-84b0-7c92f193c873/GCF_003591515.1_ASM359151v1_genomic.fna.gz --refList GCF_003591515.1_ASM359151v1_genomic.fna/target_genomes.txt --output GCF_003591515.1_ASM359151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:40,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:40,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:40,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:40,831] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:40,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:40,831] [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
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	100.0	1564	1567	95	conclusive
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	79.9138	588	1567	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.7627	671	1567	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	79.6925	655	1567	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	79.3557	535	1567	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.2996	527	1567	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.1438	451	1567	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.9079	502	1567	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	78.8065	455	1567	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.6973	456	1567	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	78.6337	476	1567	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	78.483	440	1567	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.4172	428	1567	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	78.3192	392	1567	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	77.8997	421	1567	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	77.8514	329	1567	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.7385	163	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:40,833] [INFO] DFAST Taxonomy check result was written to GCF_003591515.1_ASM359151v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:40,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:40,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:40,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/checkm_data
[2024-01-24 13:31:40,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:40,880] [INFO] Task started: CheckM
[2024-01-24 13:31:40,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003591515.1_ASM359151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003591515.1_ASM359151v1_genomic.fna/checkm_input GCF_003591515.1_ASM359151v1_genomic.fna/checkm_result
[2024-01-24 13:32:23,279] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:23,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:23,300] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:23,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:23,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003591515.1_ASM359151v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:23,302] [INFO] Task started: Blastn
[2024-01-24 13:32:23,302] [INFO] Running command: blastn -query GCF_003591515.1_ASM359151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa323a6b-bf52-4b8e-b38e-81430adc3d43/dqc_reference/reference_markers_gtdb.fasta -out GCF_003591515.1_ASM359151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:24,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:24,814] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:24,815] [INFO] Target genome list was writen to GCF_003591515.1_ASM359151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:24,825] [INFO] Task started: fastANI
[2024-01-24 13:32:24,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg11f368d6-a986-4a93-84b0-7c92f193c873/GCF_003591515.1_ASM359151v1_genomic.fna.gz --refList GCF_003591515.1_ASM359151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003591515.1_ASM359151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:34,520] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:34,530] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:34,530] [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_003591515.1	s__Paracoccus sp003591515	100.0	1564	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003007735.2	s__Paracoccus marinus_A	81.4254	746	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697785.1	s__Paracoccus alkanivorans	81.4078	811	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156835.1	s__Paracoccus saliphilus	81.2126	741	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110285.1	s__Paracoccus alcaliphilus	79.9469	584	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	79.7619	673	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018860165.1	s__Paracoccus sp018860165	79.5972	579	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002294185.1	s__Paracoccus sp002294185	79.189	489	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_017744015.1	s__Paracoccus sp002732665	79.0625	554	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_900101865.1	s__Paracoccus isoporae	78.3029	393	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	77.9082	420	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:34,532] [INFO] GTDB search result was written to GCF_003591515.1_ASM359151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:34,533] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:34,536] [INFO] DFAST_QC result json was written to GCF_003591515.1_ASM359151v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:34,536] [INFO] DFAST_QC completed!
[2024-01-24 13:32:34,537] [INFO] Total running time: 0h1m22s