[2024-01-25 18:12:50,446] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:50,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:50,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference
[2024-01-25 18:12:51,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:51,578] [INFO] Task started: Prodigal
[2024-01-25 18:12:51,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg665ab06b-53eb-4138-8e94-2aa002aaba17/GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/cds.fna -a GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:59,765] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:59,765] [INFO] Task started: HMMsearch
[2024-01-25 18:12:59,765] [INFO] Running command: hmmsearch --tblout GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/reference_markers.hmm GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:59,957] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:59,958] [INFO] Found 6/6 markers.
[2024-01-25 18:12:59,983] [INFO] Query marker FASTA was written to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:12:59,984] [INFO] Task started: Blastn
[2024-01-25 18:12:59,984] [INFO] Running command: blastn -query GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/reference_markers.fasta -out GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:00,767] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:00,770] [INFO] Selected 17 target genomes.
[2024-01-25 18:13:00,770] [INFO] Target genome list was writen to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:13:00,780] [INFO] Task started: fastANI
[2024-01-25 18:13:00,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg665ab06b-53eb-4138-8e94-2aa002aaba17/GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna.gz --refList GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:12,929] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:12,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:12,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:12,939] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:12,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:12,939] [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
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	100.0	1020	1022	95	conclusive
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	79.3843	510	1022	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.8301	498	1022	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.5805	219	1022	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.0373	177	1022	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.0366	175	1022	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.8567	205	1022	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.17	93	1022	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	76.0039	78	1022	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.9959	103	1022	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	75.9301	99	1022	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.8903	70	1022	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	75.8281	86	1022	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	75.7639	79	1022	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.6493	89	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:12,941] [INFO] DFAST Taxonomy check result was written to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:13:12,942] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:12,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:12,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/checkm_data
[2024-01-25 18:13:12,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:12,976] [INFO] Task started: CheckM
[2024-01-25 18:13:12,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/checkm_input GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:13:41,487] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:41,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:41,507] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:41,508] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:41,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:13:41,508] [INFO] Task started: Blastn
[2024-01-25 18:13:41,508] [INFO] Running command: blastn -query GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgced8a7b4-865e-42b7-88c6-e6a1b871f75b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:43,009] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:43,011] [INFO] Selected 11 target genomes.
[2024-01-25 18:13:43,012] [INFO] Target genome list was writen to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:43,031] [INFO] Task started: fastANI
[2024-01-25 18:13:43,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg665ab06b-53eb-4138-8e94-2aa002aaba17/GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna.gz --refList GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:50,209] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:50,218] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:50,219] [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_900103475.1	s__Maricaulis salignorans	100.0	1020	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003634045.1	s__Maricaulis maris	79.3933	509	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_016817355.1	s__Maricaulis parjimensis	79.2034	458	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	79.1023	495	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	79.0996	494	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_017642925.1	s__Maricaulis sp017642925	78.823	521	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	78.8132	500	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	78.7618	438	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	78.6783	373	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_001657295.1	s__Oceanicaulis sp001657295	76.9964	153	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124255.1	s__CADEEL01 sp016124255	75.531	72	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__CADEEL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:50,221] [INFO] GTDB search result was written to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:50,221] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:50,228] [INFO] DFAST_QC result json was written to GCF_900103475.1_IMG-taxon_2634166316_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:13:50,228] [INFO] DFAST_QC completed!
[2024-01-25 18:13:50,228] [INFO] Total running time: 0h0m60s