[2024-01-24 12:16:08,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference
[2024-01-24 12:16:09,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,543] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,544] [INFO] Running command: gunzip -c /var/lib/cwl/stgf353baaa-dd94-41d7-be91-4c3a9f3dbe5a/GCF_004348265.1_ASM434826v1_genomic.fna.gz | prodigal -d GCF_004348265.1_ASM434826v1_genomic.fna/cds.fna -a GCF_004348265.1_ASM434826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:23,649] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:23,650] [INFO] Task started: HMMsearch
[2024-01-24 12:16:23,650] [INFO] Running command: hmmsearch --tblout GCF_004348265.1_ASM434826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/reference_markers.hmm GCF_004348265.1_ASM434826v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:23,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:23,960] [INFO] Found 6/6 markers.
[2024-01-24 12:16:24,010] [INFO] Query marker FASTA was written to GCF_004348265.1_ASM434826v1_genomic.fna/markers.fasta
[2024-01-24 12:16:24,010] [INFO] Task started: Blastn
[2024-01-24 12:16:24,011] [INFO] Running command: blastn -query GCF_004348265.1_ASM434826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/reference_markers.fasta -out GCF_004348265.1_ASM434826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:25,013] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:25,016] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:25,016] [INFO] Target genome list was writen to GCF_004348265.1_ASM434826v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:25,024] [INFO] Task started: fastANI
[2024-01-24 12:16:25,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgf353baaa-dd94-41d7-be91-4c3a9f3dbe5a/GCF_004348265.1_ASM434826v1_genomic.fna.gz --refList GCF_004348265.1_ASM434826v1_genomic.fna/target_genomes.txt --output GCF_004348265.1_ASM434826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:39,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:39,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:39,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:39,423] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:39,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:39,423] [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 segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	100.0	1723	1734	95	conclusive
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	89.1944	1348	1734	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	87.7835	1297	1734	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	87.7186	1288	1734	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	84.1445	1119	1734	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	83.9206	880	1734	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	83.6111	1006	1734	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	83.278	1017	1734	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	83.0813	993	1734	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	82.4473	973	1734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:39,425] [INFO] DFAST Taxonomy check result was written to GCF_004348265.1_ASM434826v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:39,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:39,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:39,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/checkm_data
[2024-01-24 12:16:39,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:39,481] [INFO] Task started: CheckM
[2024-01-24 12:16:39,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348265.1_ASM434826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348265.1_ASM434826v1_genomic.fna/checkm_input GCF_004348265.1_ASM434826v1_genomic.fna/checkm_result
[2024-01-24 12:17:22,958] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:22,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:22,993] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:22,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:22,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348265.1_ASM434826v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:22,995] [INFO] Task started: Blastn
[2024-01-24 12:17:22,995] [INFO] Running command: blastn -query GCF_004348265.1_ASM434826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0f01e95-cb7d-4013-ad3e-cee0fd0219da/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348265.1_ASM434826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:24,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:24,959] [INFO] Selected 13 target genomes.
[2024-01-24 12:17:24,959] [INFO] Target genome list was writen to GCF_004348265.1_ASM434826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:24,968] [INFO] Task started: fastANI
[2024-01-24 12:17:24,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgf353baaa-dd94-41d7-be91-4c3a9f3dbe5a/GCF_004348265.1_ASM434826v1_genomic.fna.gz --refList GCF_004348265.1_ASM434826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348265.1_ASM434826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:43,464] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:43,481] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:43,482] [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_004348265.1	s__Methylobacterium segetis	100.0	1723	1734	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_003173715.1	s__Methylobacterium durans	89.1785	1350	1734	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	87.7478	1300	1734	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	84.602	1092	1734	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	84.1284	1121	1734	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	83.5767	1054	1734	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	83.1418	984	1734	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	83.1316	1010	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191355.1	s__Methylobacterium sp014191355	81.4332	930	1734	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	81.3529	927	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	77.0635	327	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	76.4285	201	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:43,483] [INFO] GTDB search result was written to GCF_004348265.1_ASM434826v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:43,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:43,487] [INFO] DFAST_QC result json was written to GCF_004348265.1_ASM434826v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:43,487] [INFO] DFAST_QC completed!
[2024-01-24 12:17:43,487] [INFO] Total running time: 0h1m35s