[2024-01-24 13:31:31,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:31,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:31,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference
[2024-01-24 13:31:32,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,721] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb560c3d-e864-4862-960e-62114faf8bc0/GCF_002358085.1_ASM235808v1_genomic.fna.gz | prodigal -d GCF_002358085.1_ASM235808v1_genomic.fna/cds.fna -a GCF_002358085.1_ASM235808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:40,809] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:40,810] [INFO] Task started: HMMsearch
[2024-01-24 13:31:40,810] [INFO] Running command: hmmsearch --tblout GCF_002358085.1_ASM235808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/reference_markers.hmm GCF_002358085.1_ASM235808v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:41,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:41,108] [INFO] Found 6/6 markers.
[2024-01-24 13:31:41,144] [INFO] Query marker FASTA was written to GCF_002358085.1_ASM235808v1_genomic.fna/markers.fasta
[2024-01-24 13:31:41,145] [INFO] Task started: Blastn
[2024-01-24 13:31:41,145] [INFO] Running command: blastn -query GCF_002358085.1_ASM235808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/reference_markers.fasta -out GCF_002358085.1_ASM235808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:42,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:42,228] [INFO] Selected 19 target genomes.
[2024-01-24 13:31:42,228] [INFO] Target genome list was writen to GCF_002358085.1_ASM235808v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:42,283] [INFO] Task started: fastANI
[2024-01-24 13:31:42,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb560c3d-e864-4862-960e-62114faf8bc0/GCF_002358085.1_ASM235808v1_genomic.fna.gz --refList GCF_002358085.1_ASM235808v1_genomic.fna/target_genomes.txt --output GCF_002358085.1_ASM235808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:56,736] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:56,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:56,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:56,752] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:31:56,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:31:56,753] [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	81.8276	599	918	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	81.7925	611	918	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	81.611	607	918	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	81.1967	583	918	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	81.1805	616	918	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	80.9363	593	918	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	80.9268	620	918	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	80.7332	548	918	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	80.6389	569	918	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	80.4826	576	918	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	80.187	504	918	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	80.1839	512	918	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.4173	467	918	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.956	382	918	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.368	366	918	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.3619	384	918	95	below_threshold
Albidovulum inexpectatum	strain=DSM 12048	GCA_002927635.1	196587	196587	type	True	78.3101	354	918	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.244	348	918	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.7081	308	918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:56,754] [INFO] DFAST Taxonomy check result was written to GCF_002358085.1_ASM235808v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:56,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:56,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:56,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/checkm_data
[2024-01-24 13:31:56,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:56,786] [INFO] Task started: CheckM
[2024-01-24 13:31:56,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002358085.1_ASM235808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002358085.1_ASM235808v1_genomic.fna/checkm_input GCF_002358085.1_ASM235808v1_genomic.fna/checkm_result
[2024-01-24 13:32:26,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:26,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:27,008] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:27,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:27,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002358085.1_ASM235808v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:27,010] [INFO] Task started: Blastn
[2024-01-24 13:32:27,010] [INFO] Running command: blastn -query GCF_002358085.1_ASM235808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531722b5-64f2-42a3-94bc-722abc9d3b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_002358085.1_ASM235808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,015] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,018] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:29,018] [INFO] Target genome list was writen to GCF_002358085.1_ASM235808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:29,033] [INFO] Task started: fastANI
[2024-01-24 13:32:29,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb560c3d-e864-4862-960e-62114faf8bc0/GCF_002358085.1_ASM235808v1_genomic.fna.gz --refList GCF_002358085.1_ASM235808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002358085.1_ASM235808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:40,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:40,258] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:40,259] [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_002358085.1	s__Thioclava arenosa	100.0	916	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002452815.1	s__UBA6796 sp002452815	82.2402	652	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_001856665.1	s__LPB0142 sp001856665	81.952	637	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_014763785.1	s__SZUA-611 sp014763785	81.8419	524	918	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_003664585.1	s__Paenirhodobacter hankyongi	81.7804	612	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	81.5725	611	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_000737065.1	s__Thioclava atlantica	81.1872	583	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714535.1	s__Thioclava pacifica	80.9268	620	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	80.7256	541	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254295.1	s__Rhodobacter capsulatus	80.6548	567	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_004022215.1	s__Paenirhodobacter populi	80.3734	471	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	80.3131	453	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900217815.1	s__Rhodobacter maris	80.1367	514	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	78.9814	470	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002927635.1	s__Albidovulum inexpectatum	78.3141	353	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:40,262] [INFO] GTDB search result was written to GCF_002358085.1_ASM235808v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:40,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:40,267] [INFO] DFAST_QC result json was written to GCF_002358085.1_ASM235808v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:40,267] [INFO] DFAST_QC completed!
[2024-01-24 13:32:40,267] [INFO] Total running time: 0h1m9s