[2024-01-24 12:06:12,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference
[2024-01-24 12:06:13,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,365] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,365] [INFO] Running command: gunzip -c /var/lib/cwl/stge5c026db-4e87-4d6f-b485-ed640bb6bd7c/GCF_003173715.1_ASM317371v1_genomic.fna.gz | prodigal -d GCF_003173715.1_ASM317371v1_genomic.fna/cds.fna -a GCF_003173715.1_ASM317371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:32,354] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:32,354] [INFO] Task started: HMMsearch
[2024-01-24 12:06:32,354] [INFO] Running command: hmmsearch --tblout GCF_003173715.1_ASM317371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/reference_markers.hmm GCF_003173715.1_ASM317371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:32,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:32,749] [INFO] Found 6/6 markers.
[2024-01-24 12:06:32,806] [INFO] Query marker FASTA was written to GCF_003173715.1_ASM317371v1_genomic.fna/markers.fasta
[2024-01-24 12:06:32,807] [INFO] Task started: Blastn
[2024-01-24 12:06:32,807] [INFO] Running command: blastn -query GCF_003173715.1_ASM317371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/reference_markers.fasta -out GCF_003173715.1_ASM317371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:33,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:33,829] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:33,829] [INFO] Target genome list was writen to GCF_003173715.1_ASM317371v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:33,834] [INFO] Task started: fastANI
[2024-01-24 12:06:33,834] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c026db-4e87-4d6f-b485-ed640bb6bd7c/GCF_003173715.1_ASM317371v1_genomic.fna.gz --refList GCF_003173715.1_ASM317371v1_genomic.fna/target_genomes.txt --output GCF_003173715.1_ASM317371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,288] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,301] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:53,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:53,302] [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 durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	100.0	2259	2262	95	conclusive
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	89.1048	1354	2262	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	88.0886	1475	2262	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	88.084	1469	2262	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	83.8052	1242	2262	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	83.6449	964	2262	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	83.268	1067	2262	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	82.9156	1083	2262	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	82.7346	1061	2262	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	82.5219	984	2262	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	82.0472	928	2262	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	81.3611	1046	2262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,304] [INFO] DFAST Taxonomy check result was written to GCF_003173715.1_ASM317371v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/checkm_data
[2024-01-24 12:06:53,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:53,372] [INFO] Task started: CheckM
[2024-01-24 12:06:53,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173715.1_ASM317371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173715.1_ASM317371v1_genomic.fna/checkm_input GCF_003173715.1_ASM317371v1_genomic.fna/checkm_result
[2024-01-24 12:07:54,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:54,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,688] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:54,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:54,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173715.1_ASM317371v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:54,689] [INFO] Task started: Blastn
[2024-01-24 12:07:54,689] [INFO] Running command: blastn -query GCF_003173715.1_ASM317371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a5fdfc-e914-4320-9bda-485e017a5e35/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173715.1_ASM317371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:56,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:56,691] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:56,691] [INFO] Target genome list was writen to GCF_003173715.1_ASM317371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:56,700] [INFO] Task started: fastANI
[2024-01-24 12:07:56,700] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c026db-4e87-4d6f-b485-ed640bb6bd7c/GCF_003173715.1_ASM317371v1_genomic.fna.gz --refList GCF_003173715.1_ASM317371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173715.1_ASM317371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:14,465] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:14,482] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:14,482] [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_003173715.1	s__Methylobacterium durans	100.0	2258	2262	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_004348265.1	s__Methylobacterium segetis	89.0987	1356	2262	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	88.0899	1470	2262	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	84.2787	1192	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	83.7773	1246	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	83.1144	1143	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	82.7429	1059	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422885.1	s__Methylobacterium sp001422885	81.7766	987	2262	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	81.6815	1048	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_900234795.1	s__Methylobacterium extorquens	81.6726	1034	2262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_900103195.1	s__Methylobacterium sp900103195	81.2312	984	2262	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 12:08:14,484] [INFO] GTDB search result was written to GCF_003173715.1_ASM317371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:14,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:14,490] [INFO] DFAST_QC result json was written to GCF_003173715.1_ASM317371v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:14,491] [INFO] DFAST_QC completed!
[2024-01-24 12:08:14,491] [INFO] Total running time: 0h2m2s