[2024-01-24 13:46:00,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference
[2024-01-24 13:46:01,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:01,375] [INFO] Task started: Prodigal
[2024-01-24 13:46:01,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg615bc58d-4624-4c49-86c2-6345bbd7eb10/GCF_902141855.1_SW08-7_genomic.fna.gz | prodigal -d GCF_902141855.1_SW08-7_genomic.fna/cds.fna -a GCF_902141855.1_SW08-7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,060] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,061] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,061] [INFO] Running command: hmmsearch --tblout GCF_902141855.1_SW08-7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/reference_markers.hmm GCF_902141855.1_SW08-7_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,388] [INFO] Found 6/6 markers.
[2024-01-24 13:46:17,436] [INFO] Query marker FASTA was written to GCF_902141855.1_SW08-7_genomic.fna/markers.fasta
[2024-01-24 13:46:17,436] [INFO] Task started: Blastn
[2024-01-24 13:46:17,437] [INFO] Running command: blastn -query GCF_902141855.1_SW08-7_genomic.fna/markers.fasta -db /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/reference_markers.fasta -out GCF_902141855.1_SW08-7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:18,457] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:18,460] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:18,461] [INFO] Target genome list was writen to GCF_902141855.1_SW08-7_genomic.fna/target_genomes.txt
[2024-01-24 13:46:18,467] [INFO] Task started: fastANI
[2024-01-24 13:46:18,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg615bc58d-4624-4c49-86c2-6345bbd7eb10/GCF_902141855.1_SW08-7_genomic.fna.gz --refList GCF_902141855.1_SW08-7_genomic.fna/target_genomes.txt --output GCF_902141855.1_SW08-7_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:34,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:34,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:34,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:34,327] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:34,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:34,327] [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 dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	100.0	1981	1986	95	conclusive
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	99.9193	1822	1986	95	conclusive
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	92.0901	1436	1986	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	86.5549	1297	1986	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	86.2781	1215	1986	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	86.2743	1258	1986	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	83.0215	905	1986	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	82.9789	1192	1986	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	82.6604	1139	1986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:34,329] [INFO] DFAST Taxonomy check result was written to GCF_902141855.1_SW08-7_genomic.fna/tc_result.tsv
[2024-01-24 13:46:34,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:34,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:34,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/checkm_data
[2024-01-24 13:46:34,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:34,403] [INFO] Task started: CheckM
[2024-01-24 13:46:34,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902141855.1_SW08-7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902141855.1_SW08-7_genomic.fna/checkm_input GCF_902141855.1_SW08-7_genomic.fna/checkm_result
[2024-01-24 13:47:21,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:21,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:21,899] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:21,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:21,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902141855.1_SW08-7_genomic.fna/markers.fasta)
[2024-01-24 13:47:21,901] [INFO] Task started: Blastn
[2024-01-24 13:47:21,901] [INFO] Running command: blastn -query GCF_902141855.1_SW08-7_genomic.fna/markers.fasta -db /var/lib/cwl/stg56124e3d-2e4b-443a-8113-61c7c2b7c5ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_902141855.1_SW08-7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:23,728] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:23,733] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:23,733] [INFO] Target genome list was writen to GCF_902141855.1_SW08-7_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:23,792] [INFO] Task started: fastANI
[2024-01-24 13:47:23,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg615bc58d-4624-4c49-86c2-6345bbd7eb10/GCF_902141855.1_SW08-7_genomic.fna.gz --refList GCF_902141855.1_SW08-7_genomic.fna/target_genomes_gtdb.txt --output GCF_902141855.1_SW08-7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:44,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:44,145] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:44,146] [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_902141855.1	s__Methylobacterium dankookense	100.0	1981	1986	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_902141845.1	s__Methylobacterium symbioticum	92.0922	1436	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173735.1	s__Methylobacterium radiodurans	86.2581	1262	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	83.8013	1089	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348265.1	s__Methylobacterium segetis	83.5436	1048	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806345.1	s__Methylobacterium sp008806345	83.4198	1116	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	83.3937	1063	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_003173715.1	s__Methylobacterium durans	83.12	1152	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	83.0361	1119	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	83.0226	1159	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCA_003096615.1	s__Methylobacterium organophilum	83.0089	1181	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_003173775.1	s__Methylobacterium sp003173775	81.4771	1058	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCA_902805995.1	s__Rubellimicrobium sp902805995	75.9655	136	1986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,147] [INFO] GTDB search result was written to GCF_902141855.1_SW08-7_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:44,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:44,151] [INFO] DFAST_QC result json was written to GCF_902141855.1_SW08-7_genomic.fna/dqc_result.json
[2024-01-24 13:47:44,151] [INFO] DFAST_QC completed!
[2024-01-24 13:47:44,151] [INFO] Total running time: 0h1m44s