[2024-01-24 13:49:27,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference
[2024-01-24 13:49:28,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,833] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg609d69a7-f6ba-4072-b98e-7cfda63fd5d8/GCF_004022465.1_ASM402246v1_genomic.fna.gz | prodigal -d GCF_004022465.1_ASM402246v1_genomic.fna/cds.fna -a GCF_004022465.1_ASM402246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:40,609] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:40,610] [INFO] Task started: HMMsearch
[2024-01-24 13:49:40,610] [INFO] Running command: hmmsearch --tblout GCF_004022465.1_ASM402246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/reference_markers.hmm GCF_004022465.1_ASM402246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:40,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:40,944] [INFO] Found 6/6 markers.
[2024-01-24 13:49:40,991] [INFO] Query marker FASTA was written to GCF_004022465.1_ASM402246v1_genomic.fna/markers.fasta
[2024-01-24 13:49:40,991] [INFO] Task started: Blastn
[2024-01-24 13:49:40,991] [INFO] Running command: blastn -query GCF_004022465.1_ASM402246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/reference_markers.fasta -out GCF_004022465.1_ASM402246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,144] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:42,144] [INFO] Target genome list was writen to GCF_004022465.1_ASM402246v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:42,150] [INFO] Task started: fastANI
[2024-01-24 13:49:42,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg609d69a7-f6ba-4072-b98e-7cfda63fd5d8/GCF_004022465.1_ASM402246v1_genomic.fna.gz --refList GCF_004022465.1_ASM402246v1_genomic.fna/target_genomes.txt --output GCF_004022465.1_ASM402246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:54,725] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:54,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:54,740] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:54,741] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:54,741] [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 huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	100.0	1365	1365	95	inconclusive
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	95.1327	1182	1365	95	inconclusive
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	93.7991	1071	1365	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	81.937	702	1365	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	81.8334	686	1365	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	80.42	623	1365	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	80.4047	591	1365	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	80.3364	595	1365	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.5176	565	1365	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.3232	470	1365	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	78.4579	491	1365	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.4463	467	1365	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.958	444	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,746] [INFO] DFAST Taxonomy check result was written to GCF_004022465.1_ASM402246v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:54,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:54,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:54,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/checkm_data
[2024-01-24 13:49:54,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:54,791] [INFO] Task started: CheckM
[2024-01-24 13:49:54,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004022465.1_ASM402246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004022465.1_ASM402246v1_genomic.fna/checkm_input GCF_004022465.1_ASM402246v1_genomic.fna/checkm_result
[2024-01-24 13:51:01,160] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:01,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,183] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004022465.1_ASM402246v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,184] [INFO] Task started: Blastn
[2024-01-24 13:51:01,184] [INFO] Running command: blastn -query GCF_004022465.1_ASM402246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg508a94bd-42e0-490c-958c-0a39c7ccf215/dqc_reference/reference_markers_gtdb.fasta -out GCF_004022465.1_ASM402246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:03,502] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:03,506] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:03,507] [INFO] Target genome list was writen to GCF_004022465.1_ASM402246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:03,514] [INFO] Task started: fastANI
[2024-01-24 13:51:03,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg609d69a7-f6ba-4072-b98e-7cfda63fd5d8/GCF_004022465.1_ASM402246v1_genomic.fna.gz --refList GCF_004022465.1_ASM402246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004022465.1_ASM402246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:11,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:11,685] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:11,686] [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_004022265.1	s__Paenirhodobacter ferrireducens	95.1327	1182	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	conclusive
GCF_003664585.1	s__Paenirhodobacter hankyongi	93.808	1070	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001856665.1	s__LPB0142 sp001856665	83.2777	769	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_003249215.1	s__SZUA-611 sp003249215	82.7636	661	1365	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_000740785.1	s__Paenirhodobacter enshiensis	82.7108	699	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	82.0386	703	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_003254295.1	s__Rhodobacter capsulatus	81.9249	704	1365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	81.8931	686	1365	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 13:51:11,692] [INFO] GTDB search result was written to GCF_004022465.1_ASM402246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:11,693] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:11,698] [INFO] DFAST_QC result json was written to GCF_004022465.1_ASM402246v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:11,699] [INFO] DFAST_QC completed!
[2024-01-24 13:51:11,699] [INFO] Total running time: 0h1m44s