[2024-01-25 19:47:35,462] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference
[2024-01-25 19:47:36,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,625] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg55a263ae-6fb8-4b19-b7fd-5f0998d9cadc/GCF_003594815.1_ASM359481v1_genomic.fna.gz | prodigal -d GCF_003594815.1_ASM359481v1_genomic.fna/cds.fna -a GCF_003594815.1_ASM359481v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:45,327] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:45,328] [INFO] Task started: HMMsearch
[2024-01-25 19:47:45,328] [INFO] Running command: hmmsearch --tblout GCF_003594815.1_ASM359481v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/reference_markers.hmm GCF_003594815.1_ASM359481v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:45,550] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:45,551] [INFO] Found 6/6 markers.
[2024-01-25 19:47:45,582] [INFO] Query marker FASTA was written to GCF_003594815.1_ASM359481v1_genomic.fna/markers.fasta
[2024-01-25 19:47:45,582] [INFO] Task started: Blastn
[2024-01-25 19:47:45,582] [INFO] Running command: blastn -query GCF_003594815.1_ASM359481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/reference_markers.fasta -out GCF_003594815.1_ASM359481v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:46,537] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:46,540] [INFO] Selected 14 target genomes.
[2024-01-25 19:47:46,540] [INFO] Target genome list was writen to GCF_003594815.1_ASM359481v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:46,545] [INFO] Task started: fastANI
[2024-01-25 19:47:46,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a263ae-6fb8-4b19-b7fd-5f0998d9cadc/GCF_003594815.1_ASM359481v1_genomic.fna.gz --refList GCF_003594815.1_ASM359481v1_genomic.fna/target_genomes.txt --output GCF_003594815.1_ASM359481v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:58,474] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:58,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:58,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:58,483] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:58,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:58,484] [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 aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	100.0	1108	1113	95	conclusive
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	87.1481	816	1113	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	86.0841	788	1113	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	85.9982	787	1113	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	84.692	747	1113	95	below_threshold
Paracoccus bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	84.3119	665	1113	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	84.0594	659	1113	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	83.4823	699	1113	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	83.387	672	1113	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.8905	644	1113	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	82.1971	634	1113	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	82.0312	570	1113	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.1668	582	1113	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.4432	517	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:58,485] [INFO] DFAST Taxonomy check result was written to GCF_003594815.1_ASM359481v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:58,486] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:58,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:58,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/checkm_data
[2024-01-25 19:47:58,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:58,524] [INFO] Task started: CheckM
[2024-01-25 19:47:58,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003594815.1_ASM359481v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003594815.1_ASM359481v1_genomic.fna/checkm_input GCF_003594815.1_ASM359481v1_genomic.fna/checkm_result
[2024-01-25 19:48:33,617] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:33,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:33,663] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:33,663] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:33,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003594815.1_ASM359481v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:33,664] [INFO] Task started: Blastn
[2024-01-25 19:48:33,664] [INFO] Running command: blastn -query GCF_003594815.1_ASM359481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ed6e03-539e-4d16-ac75-fa3f79bc98d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003594815.1_ASM359481v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:35,567] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:35,570] [INFO] Selected 11 target genomes.
[2024-01-25 19:48:35,570] [INFO] Target genome list was writen to GCF_003594815.1_ASM359481v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:35,577] [INFO] Task started: fastANI
[2024-01-25 19:48:35,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a263ae-6fb8-4b19-b7fd-5f0998d9cadc/GCF_003594815.1_ASM359481v1_genomic.fna.gz --refList GCF_003594815.1_ASM359481v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003594815.1_ASM359481v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:45,660] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:45,668] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:45,668] [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_003594815.1	s__Paracoccus aestuarii	100.0	1108	1113	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_005048265.1	s__Paracoccus hibiscisoli	87.1736	814	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_006151785.1	s__Paracoccus marcusii	86.2909	721	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_004683865.2	s__Paracoccus liaowanqingii	86.0637	790	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_005048225.1	s__Paracoccus gahaiensis	86.0537	783	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787695.1	s__Paracoccus sp000787695	85.8349	716	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	84.0369	660	1113	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	84.0135	689	1113	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	83.1201	512	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	82.7264	652	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	82.1649	636	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:45,669] [INFO] GTDB search result was written to GCF_003594815.1_ASM359481v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:45,670] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:45,672] [INFO] DFAST_QC result json was written to GCF_003594815.1_ASM359481v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:45,672] [INFO] DFAST_QC completed!
[2024-01-25 19:48:45,672] [INFO] Total running time: 0h1m10s