[2024-01-24 13:33:11,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:11,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:11,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference
[2024-01-24 13:33:12,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,464] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg9520432f-6d45-415b-aaa2-2e9f257e0264/GCF_004683865.2_ASM468386v2_genomic.fna.gz | prodigal -d GCF_004683865.2_ASM468386v2_genomic.fna/cds.fna -a GCF_004683865.2_ASM468386v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:27,670] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:27,671] [INFO] Task started: HMMsearch
[2024-01-24 13:33:27,671] [INFO] Running command: hmmsearch --tblout GCF_004683865.2_ASM468386v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/reference_markers.hmm GCF_004683865.2_ASM468386v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:27,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:27,981] [INFO] Found 6/6 markers.
[2024-01-24 13:33:28,030] [INFO] Query marker FASTA was written to GCF_004683865.2_ASM468386v2_genomic.fna/markers.fasta
[2024-01-24 13:33:28,031] [INFO] Task started: Blastn
[2024-01-24 13:33:28,031] [INFO] Running command: blastn -query GCF_004683865.2_ASM468386v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/reference_markers.fasta -out GCF_004683865.2_ASM468386v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:29,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:29,091] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:29,092] [INFO] Target genome list was writen to GCF_004683865.2_ASM468386v2_genomic.fna/target_genomes.txt
[2024-01-24 13:33:29,102] [INFO] Task started: fastANI
[2024-01-24 13:33:29,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg9520432f-6d45-415b-aaa2-2e9f257e0264/GCF_004683865.2_ASM468386v2_genomic.fna.gz --refList GCF_004683865.2_ASM468386v2_genomic.fna/target_genomes.txt --output GCF_004683865.2_ASM468386v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:40,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:40,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:40,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:40,745] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:40,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:40,745] [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 liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	100.0	1631	1636	95	conclusive
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	93.2244	1112	1636	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	86.9718	966	1636	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	86.3959	939	1636	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	85.9528	789	1636	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	83.9045	845	1636	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	82.7886	708	1636	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.7871	757	1636	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.8212	654	1636	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.2358	651	1636	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.2877	545	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:40,747] [INFO] DFAST Taxonomy check result was written to GCF_004683865.2_ASM468386v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:40,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:40,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:40,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/checkm_data
[2024-01-24 13:33:40,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:40,821] [INFO] Task started: CheckM
[2024-01-24 13:33:40,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004683865.2_ASM468386v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004683865.2_ASM468386v2_genomic.fna/checkm_input GCF_004683865.2_ASM468386v2_genomic.fna/checkm_result
[2024-01-24 13:34:33,619] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:33,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:33,642] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:33,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:33,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004683865.2_ASM468386v2_genomic.fna/markers.fasta)
[2024-01-24 13:34:33,644] [INFO] Task started: Blastn
[2024-01-24 13:34:33,644] [INFO] Running command: blastn -query GCF_004683865.2_ASM468386v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0273adc5-66ba-40e2-8f97-acec65b549b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004683865.2_ASM468386v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:35,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:35,617] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:35,618] [INFO] Target genome list was writen to GCF_004683865.2_ASM468386v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:35,653] [INFO] Task started: fastANI
[2024-01-24 13:34:35,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg9520432f-6d45-415b-aaa2-2e9f257e0264/GCF_004683865.2_ASM468386v2_genomic.fna.gz --refList GCF_004683865.2_ASM468386v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004683865.2_ASM468386v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:47,012] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:47,028] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:47,029] [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_004683865.2	s__Paracoccus liaowanqingii	100.0	1632	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	conclusive
GCF_005048225.1	s__Paracoccus gahaiensis	93.2393	1111	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335005.1	s__Paracoccus sp004335005	86.9812	965	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048265.1	s__Paracoccus hibiscisoli	86.4003	939	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_003594815.1	s__Paracoccus aestuarii	85.9419	790	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151785.1	s__Paracoccus marcusii	85.8998	822	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_000787695.1	s__Paracoccus sp000787695	85.8498	847	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	83.9983	834	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869875.1	s__Paracoccus sp016869875	83.3562	627	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.0666	275	1636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:47,031] [INFO] GTDB search result was written to GCF_004683865.2_ASM468386v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:47,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:47,034] [INFO] DFAST_QC result json was written to GCF_004683865.2_ASM468386v2_genomic.fna/dqc_result.json
[2024-01-24 13:34:47,034] [INFO] DFAST_QC completed!
[2024-01-24 13:34:47,035] [INFO] Total running time: 0h1m36s