[2024-01-24 14:23:04,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,066] [INFO] DQC Reference Directory: /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference
[2024-01-24 14:23:05,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:05,462] [INFO] Task started: Prodigal
[2024-01-24 14:23:05,462] [INFO] Running command: gunzip -c /var/lib/cwl/stgff28a84c-754d-456c-9148-6fc6d680275a/GCF_019264375.1_ASM1926437v1_genomic.fna.gz | prodigal -d GCF_019264375.1_ASM1926437v1_genomic.fna/cds.fna -a GCF_019264375.1_ASM1926437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:15,846] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:15,846] [INFO] Task started: HMMsearch
[2024-01-24 14:23:15,846] [INFO] Running command: hmmsearch --tblout GCF_019264375.1_ASM1926437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/reference_markers.hmm GCF_019264375.1_ASM1926437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:16,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:16,198] [INFO] Found 6/6 markers.
[2024-01-24 14:23:16,250] [INFO] Query marker FASTA was written to GCF_019264375.1_ASM1926437v1_genomic.fna/markers.fasta
[2024-01-24 14:23:16,251] [INFO] Task started: Blastn
[2024-01-24 14:23:16,251] [INFO] Running command: blastn -query GCF_019264375.1_ASM1926437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/reference_markers.fasta -out GCF_019264375.1_ASM1926437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:17,360] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:17,364] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:17,365] [INFO] Target genome list was writen to GCF_019264375.1_ASM1926437v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:17,371] [INFO] Task started: fastANI
[2024-01-24 14:23:17,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgff28a84c-754d-456c-9148-6fc6d680275a/GCF_019264375.1_ASM1926437v1_genomic.fna.gz --refList GCF_019264375.1_ASM1926437v1_genomic.fna/target_genomes.txt --output GCF_019264375.1_ASM1926437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:28,994] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:28,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:28,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:29,008] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:29,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:29,008] [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
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	82.0502	664	1098	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	81.8855	636	1098	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	81.8125	656	1098	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	80.7141	603	1098	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	80.6767	594	1098	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	80.6313	565	1098	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	80.4994	556	1098	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	80.3926	595	1098	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	80.3635	521	1098	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	80.2988	520	1098	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	80.0026	552	1098	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.2172	454	1098	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.8868	375	1098	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.8685	374	1098	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.8432	447	1098	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.1216	338	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:29,010] [INFO] DFAST Taxonomy check result was written to GCF_019264375.1_ASM1926437v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:29,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:29,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:29,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/checkm_data
[2024-01-24 14:23:29,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:29,048] [INFO] Task started: CheckM
[2024-01-24 14:23:29,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019264375.1_ASM1926437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019264375.1_ASM1926437v1_genomic.fna/checkm_input GCF_019264375.1_ASM1926437v1_genomic.fna/checkm_result
[2024-01-24 14:24:03,495] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:03,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:03,522] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:03,523] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:03,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019264375.1_ASM1926437v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:03,523] [INFO] Task started: Blastn
[2024-01-24 14:24:03,524] [INFO] Running command: blastn -query GCF_019264375.1_ASM1926437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd4a5a5-c687-4783-9b70-5398e20b6785/dqc_reference/reference_markers_gtdb.fasta -out GCF_019264375.1_ASM1926437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:05,210] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:05,213] [INFO] Selected 12 target genomes.
[2024-01-24 14:24:05,213] [INFO] Target genome list was writen to GCF_019264375.1_ASM1926437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:05,222] [INFO] Task started: fastANI
[2024-01-24 14:24:05,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgff28a84c-754d-456c-9148-6fc6d680275a/GCF_019264375.1_ASM1926437v1_genomic.fna.gz --refList GCF_019264375.1_ASM1926437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019264375.1_ASM1926437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:14,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:14,125] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:24:14,126] [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_001856665.1	s__LPB0142 sp001856665	82.5116	712	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_002452815.1	s__UBA6796 sp002452815	82.32	674	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_002358085.1	s__Thioclava arenosa	82.0682	638	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	82.0428	665	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	81.9522	556	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	81.8791	635	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCA_003249215.1	s__SZUA-611 sp003249215	81.7495	572	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217355.1	s__Rhodobacter viridis	80.6367	564	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	80.4976	484	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	80.4827	566	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	80.0931	505	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_900217815.1	s__Rhodobacter maris	79.8299	549	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:14,128] [INFO] GTDB search result was written to GCF_019264375.1_ASM1926437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:14,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:14,132] [INFO] DFAST_QC result json was written to GCF_019264375.1_ASM1926437v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:14,132] [INFO] DFAST_QC completed!
[2024-01-24 14:24:14,132] [INFO] Total running time: 0h1m10s