[2024-01-24 14:20:00,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:00,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:00,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference
[2024-01-24 14:20:01,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,695] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9a68157-e35f-4876-a81f-be0f13043c99/GCF_026162625.1_ASM2616262v1_genomic.fna.gz | prodigal -d GCF_026162625.1_ASM2616262v1_genomic.fna/cds.fna -a GCF_026162625.1_ASM2616262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:12,876] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:12,877] [INFO] Task started: HMMsearch
[2024-01-24 14:20:12,877] [INFO] Running command: hmmsearch --tblout GCF_026162625.1_ASM2616262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/reference_markers.hmm GCF_026162625.1_ASM2616262v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:13,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:13,154] [INFO] Found 6/6 markers.
[2024-01-24 14:20:13,194] [INFO] Query marker FASTA was written to GCF_026162625.1_ASM2616262v1_genomic.fna/markers.fasta
[2024-01-24 14:20:13,195] [INFO] Task started: Blastn
[2024-01-24 14:20:13,195] [INFO] Running command: blastn -query GCF_026162625.1_ASM2616262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/reference_markers.fasta -out GCF_026162625.1_ASM2616262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:14,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:14,223] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:14,223] [INFO] Target genome list was writen to GCF_026162625.1_ASM2616262v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:14,269] [INFO] Task started: fastANI
[2024-01-24 14:20:14,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a68157-e35f-4876-a81f-be0f13043c99/GCF_026162625.1_ASM2616262v1_genomic.fna.gz --refList GCF_026162625.1_ASM2616262v1_genomic.fna/target_genomes.txt --output GCF_026162625.1_ASM2616262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:26,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:26,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:26,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:26,159] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:26,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:26,160] [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	84.1247	837	1260	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	83.9682	778	1260	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	83.8642	815	1260	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	83.8502	711	1260	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	83.2501	660	1260	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	83.0011	748	1260	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	82.816	754	1260	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	82.6331	753	1260	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	82.5599	673	1260	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.4315	680	1260	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.9876	690	1260	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.9505	700	1260	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.2537	610	1260	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.7583	598	1260	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3835	478	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:26,161] [INFO] DFAST Taxonomy check result was written to GCF_026162625.1_ASM2616262v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:26,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:26,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:26,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/checkm_data
[2024-01-24 14:20:26,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:26,205] [INFO] Task started: CheckM
[2024-01-24 14:20:26,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026162625.1_ASM2616262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026162625.1_ASM2616262v1_genomic.fna/checkm_input GCF_026162625.1_ASM2616262v1_genomic.fna/checkm_result
[2024-01-24 14:21:06,172] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:06,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:06,193] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:06,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:06,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026162625.1_ASM2616262v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:06,194] [INFO] Task started: Blastn
[2024-01-24 14:21:06,194] [INFO] Running command: blastn -query GCF_026162625.1_ASM2616262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ef65d15-109f-4a31-953e-738b2e6eb191/dqc_reference/reference_markers_gtdb.fasta -out GCF_026162625.1_ASM2616262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:08,118] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:08,121] [INFO] Selected 12 target genomes.
[2024-01-24 14:21:08,122] [INFO] Target genome list was writen to GCF_026162625.1_ASM2616262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:08,132] [INFO] Task started: fastANI
[2024-01-24 14:21:08,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a68157-e35f-4876-a81f-be0f13043c99/GCF_026162625.1_ASM2616262v1_genomic.fna.gz --refList GCF_026162625.1_ASM2616262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026162625.1_ASM2616262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:18,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:18,124] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:18,124] [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_006151785.1	s__Paracoccus marcusii	84.1485	716	1260	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	84.0961	839	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_005048265.1	s__Paracoccus hibiscisoli	83.9803	777	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_005048225.1	s__Paracoccus gahaiensis	83.8866	813	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594815.1	s__Paracoccus aestuarii	83.8295	712	1260	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	83.6964	720	1260	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	83.6569	759	1260	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	83.3458	591	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056335.1	s__Paracoccus indicus	83.0011	748	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102505.1	s__Paracoccus tibetensis	82.8273	753	1260	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	82.5837	671	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	81.9371	701	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:18,126] [INFO] GTDB search result was written to GCF_026162625.1_ASM2616262v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:18,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:18,131] [INFO] DFAST_QC result json was written to GCF_026162625.1_ASM2616262v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:18,131] [INFO] DFAST_QC completed!
[2024-01-24 14:21:18,131] [INFO] Total running time: 0h1m18s