[2024-01-24 12:13:25,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:25,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:25,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference
[2024-01-24 12:13:26,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,643] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg106f68d3-39f1-4821-8a6d-98ac24261f4b/GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/cds.fna -a GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:34,521] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:34,522] [INFO] Task started: HMMsearch
[2024-01-24 12:13:34,522] [INFO] Running command: hmmsearch --tblout GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/reference_markers.hmm GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:34,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:34,899] [INFO] Found 6/6 markers.
[2024-01-24 12:13:34,949] [INFO] Query marker FASTA was written to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:34,950] [INFO] Task started: Blastn
[2024-01-24 12:13:34,950] [INFO] Running command: blastn -query GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/reference_markers.fasta -out GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:35,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:35,657] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:35,658] [INFO] Target genome list was writen to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:35,754] [INFO] Task started: fastANI
[2024-01-24 12:13:35,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg106f68d3-39f1-4821-8a6d-98ac24261f4b/GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna.gz --refList GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:48,866] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:48,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:48,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:48,877] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:48,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:48,877] [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
Methylobacillus rhizosphaerae	strain=Ca-68	GCA_900187985.1	551994	551994	type	True	100.0	781	781	95	conclusive
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	80.1518	427	781	95	below_threshold
Methylobacillus methanolivorans	strain=VKM B-3037	GCA_020531845.1	1848927	1848927	type	True	79.5845	379	781	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	79.2903	380	781	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	78.8815	319	781	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	78.8808	333	781	95	below_threshold
Methylobacillus gramineus	strain=VKM B-2591	GCA_020532675.1	755169	755169	type	True	78.6789	331	781	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	77.9703	200	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:48,887] [INFO] DFAST Taxonomy check result was written to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:48,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:48,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:48,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/checkm_data
[2024-01-24 12:13:48,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:48,928] [INFO] Task started: CheckM
[2024-01-24 12:13:48,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/checkm_input GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:18,567] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:18,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:18,589] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:18,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:18,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:18,590] [INFO] Task started: Blastn
[2024-01-24 12:14:18,590] [INFO] Running command: blastn -query GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cd21813-085e-499a-8d9a-e15da502e908/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:19,553] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:19,557] [INFO] Selected 21 target genomes.
[2024-01-24 12:14:19,558] [INFO] Target genome list was writen to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:19,721] [INFO] Task started: fastANI
[2024-01-24 12:14:19,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg106f68d3-39f1-4821-8a6d-98ac24261f4b/GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna.gz --refList GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:29,493] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:29,509] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:29,509] [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_900187985.1	s__Methylobacillus rhizosphaerae	100.0	781	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013705.1	s__Methylobacillus flagellatus	79.298	381	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCF_000617925.1	s__Methylobacillus glycogenes	78.8956	318	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858335.1	s__Methylovorus glucosotrophus	77.7996	197	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylovorus	95.0	97.11	97.01	0.92	0.92	3	-
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	77.3161	155	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842435.1	s__UBA6140 sp002842435	77.3115	140	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479405.1	s__UBA6140 sp002479405	77.0877	119	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423265.1	s__UBA6140 sp002423265	76.9098	82	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799735.1	s__Methylotenera sp000799735	76.7529	81	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023705.1	s__Methylotenera mobilis	76.7417	57	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112435.1	s__Novimethylophilus kurashikiensis	76.7221	88	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Novimethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424665.1	s__Methylophilus sp001424665	76.3038	102	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	98.77	97.54	0.97	0.93	3	-
GCF_000971475.1	s__Sulfuricella sp000971475	75.9543	51	781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:29,511] [INFO] GTDB search result was written to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:29,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:29,516] [INFO] DFAST_QC result json was written to GCF_900187985.1_IMG-taxon_2657245330_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:29,516] [INFO] DFAST_QC completed!
[2024-01-24 12:14:29,516] [INFO] Total running time: 0h1m4s