[2024-01-24 14:55:26,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference
[2024-01-24 14:55:28,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,177] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgf56a2a77-a57f-41fb-8ace-df71317dfed0/GCF_005048225.1_ASM504822v1_genomic.fna.gz | prodigal -d GCF_005048225.1_ASM504822v1_genomic.fna/cds.fna -a GCF_005048225.1_ASM504822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:40,750] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:40,750] [INFO] Task started: HMMsearch
[2024-01-24 14:55:40,750] [INFO] Running command: hmmsearch --tblout GCF_005048225.1_ASM504822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/reference_markers.hmm GCF_005048225.1_ASM504822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:40,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:41,000] [INFO] Found 6/6 markers.
[2024-01-24 14:55:41,040] [INFO] Query marker FASTA was written to GCF_005048225.1_ASM504822v1_genomic.fna/markers.fasta
[2024-01-24 14:55:41,040] [INFO] Task started: Blastn
[2024-01-24 14:55:41,040] [INFO] Running command: blastn -query GCF_005048225.1_ASM504822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/reference_markers.fasta -out GCF_005048225.1_ASM504822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:42,148] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:42,152] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:42,152] [INFO] Target genome list was writen to GCF_005048225.1_ASM504822v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:42,165] [INFO] Task started: fastANI
[2024-01-24 14:55:42,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56a2a77-a57f-41fb-8ace-df71317dfed0/GCF_005048225.1_ASM504822v1_genomic.fna.gz --refList GCF_005048225.1_ASM504822v1_genomic.fna/target_genomes.txt --output GCF_005048225.1_ASM504822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:53,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:53,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:53,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:53,136] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:53,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:53,136] [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 gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	100.0	1357	1358	95	conclusive
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	93.1219	1119	1358	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	86.9799	969	1358	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	86.4569	908	1358	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	86.0577	766	1358	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	83.8564	812	1358	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.8154	722	1358	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	82.475	712	1358	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.6864	639	1358	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.3408	653	1358	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3754	553	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:53,141] [INFO] DFAST Taxonomy check result was written to GCF_005048225.1_ASM504822v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:53,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:53,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:53,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/checkm_data
[2024-01-24 14:55:53,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:53,187] [INFO] Task started: CheckM
[2024-01-24 14:55:53,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005048225.1_ASM504822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005048225.1_ASM504822v1_genomic.fna/checkm_input GCF_005048225.1_ASM504822v1_genomic.fna/checkm_result
[2024-01-24 14:56:33,783] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:33,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:33,804] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:33,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:33,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005048225.1_ASM504822v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:33,805] [INFO] Task started: Blastn
[2024-01-24 14:56:33,805] [INFO] Running command: blastn -query GCF_005048225.1_ASM504822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e8ca8c-ecf0-4905-838d-df63c1c618ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_005048225.1_ASM504822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:35,845] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:35,851] [INFO] Selected 9 target genomes.
[2024-01-24 14:56:35,851] [INFO] Target genome list was writen to GCF_005048225.1_ASM504822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:35,859] [INFO] Task started: fastANI
[2024-01-24 14:56:35,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56a2a77-a57f-41fb-8ace-df71317dfed0/GCF_005048225.1_ASM504822v1_genomic.fna.gz --refList GCF_005048225.1_ASM504822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005048225.1_ASM504822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:45,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:45,462] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:45,463] [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_005048225.1	s__Paracoccus gahaiensis	100.0	1357	1358	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_004683865.2	s__Paracoccus liaowanqingii	93.1474	1117	1358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_004335005.1	s__Paracoccus sp004335005	86.9617	970	1358	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	86.4322	910	1358	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	86.1094	762	1358	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	85.7102	805	1358	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	85.6812	837	1358	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	83.9849	794	1358	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	83.3305	603	1358	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 14:56:45,465] [INFO] GTDB search result was written to GCF_005048225.1_ASM504822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:45,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:45,469] [INFO] DFAST_QC result json was written to GCF_005048225.1_ASM504822v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:45,469] [INFO] DFAST_QC completed!
[2024-01-24 14:56:45,469] [INFO] Total running time: 0h1m19s