[2024-01-24 13:22:30,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:30,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:30,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference
[2024-01-24 13:22:32,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,277] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b959b40-dbfb-4ca2-85ec-27f799d99ffa/GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/cds.fna -a GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:43,918] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:43,918] [INFO] Task started: HMMsearch
[2024-01-24 13:22:43,918] [INFO] Running command: hmmsearch --tblout GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/reference_markers.hmm GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:44,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:44,189] [INFO] Found 6/6 markers.
[2024-01-24 13:22:44,224] [INFO] Query marker FASTA was written to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:44,224] [INFO] Task started: Blastn
[2024-01-24 13:22:44,224] [INFO] Running command: blastn -query GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/reference_markers.fasta -out GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:45,089] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:45,092] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:45,092] [INFO] Target genome list was writen to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:46,150] [INFO] Task started: fastANI
[2024-01-24 13:22:46,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b959b40-dbfb-4ca2-85ec-27f799d99ffa/GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna.gz --refList GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:57,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:57,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:57,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:57,071] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:57,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:57,071] [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
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	82.7078	808	1245	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	82.368	781	1245	95	below_threshold
Rhodobacter aestuarii	strain=JA296	GCA_003053525.1	453582	453582	type	True	81.6445	777	1245	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	81.6023	779	1245	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	81.2145	639	1245	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	81.1418	636	1245	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	81.0679	655	1245	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	79.6072	528	1245	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	78.8243	490	1245	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.1009	366	1245	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.0829	407	1245	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.7374	315	1245	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.6895	376	1245	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.3911	316	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,073] [INFO] DFAST Taxonomy check result was written to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:57,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:57,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:57,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/checkm_data
[2024-01-24 13:22:57,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:57,121] [INFO] Task started: CheckM
[2024-01-24 13:22:57,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/checkm_input GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:41,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:41,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:41,775] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:41,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:41,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:41,776] [INFO] Task started: Blastn
[2024-01-24 13:23:41,776] [INFO] Running command: blastn -query GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg710efa00-1229-431c-bea1-3e967b08b440/dqc_reference/reference_markers_gtdb.fasta -out GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:43,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:43,331] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:43,331] [INFO] Target genome list was writen to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:43,639] [INFO] Task started: fastANI
[2024-01-24 13:23:43,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b959b40-dbfb-4ca2-85ec-27f799d99ffa/GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna.gz --refList GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:52,594] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:52,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:52,612] [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_900217815.1	s__Rhodobacter maris	100.0	1241	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003254295.1	s__Rhodobacter capsulatus	82.7349	805	1245	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	82.5978	821	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021865.1	s__Rhodobacter capsulatus_B	82.5813	833	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.13	98.02	0.96	0.92	8	-
GCF_003217355.1	s__Rhodobacter viridis	82.3718	781	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156655.1	s__Rhodobacter aestuarii	81.5893	781	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	98.72	97.43	0.96	0.93	3	-
GCF_001856665.1	s__LPB0142 sp001856665	81.5851	674	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	81.0545	656	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249215.1	s__SZUA-611 sp003249215	80.6145	539	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	80.2015	567	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:52,614] [INFO] GTDB search result was written to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:52,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:52,619] [INFO] DFAST_QC result json was written to GCF_900217815.1_IMG-taxon_2739368070_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:52,619] [INFO] DFAST_QC completed!
[2024-01-24 13:23:52,620] [INFO] Total running time: 0h1m22s