[2024-01-24 12:29:27,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:27,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:27,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference
[2024-01-24 12:29:28,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,738] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg761ef4fb-962d-4330-a228-0ddd362cc374/GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/cds.fna -a GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:45,122] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:45,122] [INFO] Task started: HMMsearch
[2024-01-24 12:29:45,122] [INFO] Running command: hmmsearch --tblout GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/reference_markers.hmm GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:45,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:45,571] [INFO] Found 6/6 markers.
[2024-01-24 12:29:45,622] [INFO] Query marker FASTA was written to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:29:45,622] [INFO] Task started: Blastn
[2024-01-24 12:29:45,622] [INFO] Running command: blastn -query GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/reference_markers.fasta -out GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:46,741] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:46,745] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:46,745] [INFO] Target genome list was writen to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:29:46,754] [INFO] Task started: fastANI
[2024-01-24 12:29:46,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg761ef4fb-962d-4330-a228-0ddd362cc374/GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna.gz --refList GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:04,639] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:04,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:04,650] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:04,650] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:04,650] [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
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	100.0	1979	1981	95	conclusive
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	87.0269	1424	1981	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	86.9897	1470	1981	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	86.9458	1429	1981	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	86.8992	1461	1981	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	86.6613	1375	1981	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	86.5895	1415	1981	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	86.2084	1375	1981	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	85.2856	1345	1981	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.4943	1039	1981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,652] [INFO] DFAST Taxonomy check result was written to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:30:04,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:04,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:04,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/checkm_data
[2024-01-24 12:30:04,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:04,721] [INFO] Task started: CheckM
[2024-01-24 12:30:04,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/checkm_input GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:30:55,020] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:55,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:55,045] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:55,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:55,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:30:55,046] [INFO] Task started: Blastn
[2024-01-24 12:30:55,047] [INFO] Running command: blastn -query GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgafec158a-569d-4f5c-953e-cfef1a2eca1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:57,103] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:57,106] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:57,107] [INFO] Target genome list was writen to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:57,118] [INFO] Task started: fastANI
[2024-01-24 12:30:57,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg761ef4fb-962d-4330-a228-0ddd362cc374/GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna.gz --refList GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:12,149] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:12,163] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:12,164] [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_900103445.1	s__Methylobacterium phyllostachyos	100.0	1979	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009806555.1	s__Methylobacterium sp009806555	89.902	1491	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	87.0209	1438	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_900112625.1	s__Methylobacterium sp900112625	86.9414	1418	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_014873335.1	s__Methylobacterium sp014873335	86.8449	1398	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000364445.2	s__Methylobacterium mesophilicum	86.7533	1423	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138435.1	s__Methylobacterium fujisawaense	86.7289	1384	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_017833295.1	s__Methylobacterium sp017833295	86.6781	1396	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103195.1	s__Methylobacterium sp900103195	86.5485	1390	1981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:12,165] [INFO] GTDB search result was written to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:12,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:12,169] [INFO] DFAST_QC result json was written to GCF_900103445.1_IMG-taxon_2651870120_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:31:12,169] [INFO] DFAST_QC completed!
[2024-01-24 12:31:12,169] [INFO] Total running time: 0h1m45s