[2024-01-25 20:13:35,830] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,831] [INFO] DQC Reference Directory: /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference
[2024-01-25 20:13:36,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,977] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b1efab6-fc87-4797-a0b5-2a8309554e1d/GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/cds.fna -a GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:44,709] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:44,709] [INFO] Task started: HMMsearch
[2024-01-25 20:13:44,709] [INFO] Running command: hmmsearch --tblout GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/reference_markers.hmm GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:44,961] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:44,962] [INFO] Found 6/6 markers.
[2024-01-25 20:13:44,985] [INFO] Query marker FASTA was written to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:13:44,986] [INFO] Task started: Blastn
[2024-01-25 20:13:44,986] [INFO] Running command: blastn -query GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/reference_markers.fasta -out GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:45,564] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:45,567] [INFO] Selected 17 target genomes.
[2024-01-25 20:13:45,567] [INFO] Target genome list was writen to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:13:45,574] [INFO] Task started: fastANI
[2024-01-25 20:13:45,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b1efab6-fc87-4797-a0b5-2a8309554e1d/GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna.gz --refList GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:54,148] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:54,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:54,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:54,156] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:54,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:54,156] [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
Methylophilus rhizosphaerae	strain=CBMB127	GCA_900100975.1	492660	492660	type	True	100.0	915	915	95	conclusive
Methylophilus methylotrophus	strain=ATCC 53528	GCA_000378225.1	17	17	type	True	80.0911	494	915	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	77.2612	149	915	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	77.2262	97	915	95	below_threshold
Methylotenera oryzisoli	strain=La3113	GCA_004661485.1	2080758	2080758	type	True	77.1402	79	915	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	77.0735	130	915	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.9532	119	915	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	76.7753	94	915	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	76.7356	143	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:54,157] [INFO] DFAST Taxonomy check result was written to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:13:54,158] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:54,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:54,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/checkm_data
[2024-01-25 20:13:54,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:54,187] [INFO] Task started: CheckM
[2024-01-25 20:13:54,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/checkm_input GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:14:21,482] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:21,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:21,503] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:21,503] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:21,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:14:21,504] [INFO] Task started: Blastn
[2024-01-25 20:14:21,504] [INFO] Running command: blastn -query GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga505f237-d41f-4aeb-9bdc-a30c777f02ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:22,372] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:22,375] [INFO] Selected 11 target genomes.
[2024-01-25 20:14:22,375] [INFO] Target genome list was writen to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:22,397] [INFO] Task started: fastANI
[2024-01-25 20:14:22,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b1efab6-fc87-4797-a0b5-2a8309554e1d/GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna.gz --refList GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:29,884] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:29,892] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:29,892] [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_900100975.1	s__Methylophilus rhizosphaerae	100.0	915	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015354445.1	s__Methylophilus sp015354445	80.6451	541	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354345.1	s__Methylophilus sp015354345	80.5135	523	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384155.1	s__Methylophilus sp000384155	80.5126	535	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	97.28	96.56	0.94	0.91	6	-
GCF_001183865.1	s__Methylophilus sp001183865	80.3283	475	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424665.1	s__Methylophilus sp001424665	80.1292	518	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	98.77	97.54	0.97	0.93	3	-
GCF_000378225.1	s__Methylophilus methylotrophus	80.0911	494	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	96.53	96.51	0.88	0.88	3	-
GCF_000515275.1	s__Methylophilus sp000515275	80.0134	498	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015755.1	s__Methylophilus sp008015755	79.8389	449	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354335.1	s__Methylophilus sp015354335	79.818	463	915	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:29,893] [INFO] GTDB search result was written to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:29,894] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:29,896] [INFO] DFAST_QC result json was written to GCF_900100975.1_IMG-taxon_2654588194_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:14:29,896] [INFO] DFAST_QC completed!
[2024-01-25 20:14:29,896] [INFO] Total running time: 0h0m54s