[2024-01-24 13:28:11,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference
[2024-01-24 13:28:12,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,821] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg92923eab-44cd-4bff-bda4-8f704323ea4f/GCF_902141845.1_CECT_9862_genomic.fna.gz | prodigal -d GCF_902141845.1_CECT_9862_genomic.fna/cds.fna -a GCF_902141845.1_CECT_9862_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:27,811] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:27,812] [INFO] Task started: HMMsearch
[2024-01-24 13:28:27,812] [INFO] Running command: hmmsearch --tblout GCF_902141845.1_CECT_9862_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/reference_markers.hmm GCF_902141845.1_CECT_9862_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:28,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:28,121] [INFO] Found 6/6 markers.
[2024-01-24 13:28:28,173] [INFO] Query marker FASTA was written to GCF_902141845.1_CECT_9862_genomic.fna/markers.fasta
[2024-01-24 13:28:28,174] [INFO] Task started: Blastn
[2024-01-24 13:28:28,174] [INFO] Running command: blastn -query GCF_902141845.1_CECT_9862_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/reference_markers.fasta -out GCF_902141845.1_CECT_9862_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:29,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:29,265] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:29,266] [INFO] Target genome list was writen to GCF_902141845.1_CECT_9862_genomic.fna/target_genomes.txt
[2024-01-24 13:28:29,319] [INFO] Task started: fastANI
[2024-01-24 13:28:29,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg92923eab-44cd-4bff-bda4-8f704323ea4f/GCF_902141845.1_CECT_9862_genomic.fna.gz --refList GCF_902141845.1_CECT_9862_genomic.fna/target_genomes.txt --output GCF_902141845.1_CECT_9862_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:44,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:44,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:44,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:45,003] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:45,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:45,003] [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 symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	100.0	1893	1908	95	conclusive
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	92.1573	1446	1908	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	92.0772	1352	1908	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	86.0419	1206	1908	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	85.6297	1171	1908	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	85.4254	1152	1908	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	82.9066	1001	1908	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	82.7705	1037	1908	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	82.52	866	1908	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	82.0839	1045	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:45,006] [INFO] DFAST Taxonomy check result was written to GCF_902141845.1_CECT_9862_genomic.fna/tc_result.tsv
[2024-01-24 13:28:45,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:45,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:45,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/checkm_data
[2024-01-24 13:28:45,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:45,069] [INFO] Task started: CheckM
[2024-01-24 13:28:45,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902141845.1_CECT_9862_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902141845.1_CECT_9862_genomic.fna/checkm_input GCF_902141845.1_CECT_9862_genomic.fna/checkm_result
[2024-01-24 13:29:32,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:32,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:32,024] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:32,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:32,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902141845.1_CECT_9862_genomic.fna/markers.fasta)
[2024-01-24 13:29:32,025] [INFO] Task started: Blastn
[2024-01-24 13:29:32,025] [INFO] Running command: blastn -query GCF_902141845.1_CECT_9862_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3a4c26-2b0a-428d-b95c-2378997d2c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_902141845.1_CECT_9862_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:34,200] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:34,204] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:34,205] [INFO] Target genome list was writen to GCF_902141845.1_CECT_9862_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:34,330] [INFO] Task started: fastANI
[2024-01-24 13:29:34,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg92923eab-44cd-4bff-bda4-8f704323ea4f/GCF_902141845.1_CECT_9862_genomic.fna.gz --refList GCF_902141845.1_CECT_9862_genomic.fna/target_genomes_gtdb.txt --output GCF_902141845.1_CECT_9862_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:57,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:57,729] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:57,729] [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_902141845.1	s__Methylobacterium symbioticum	100.0	1893	1908	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_902141855.1	s__Methylobacterium dankookense	92.1655	1445	1908	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	85.6277	1172	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	83.3042	1007	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_007992195.1	s__Methylobacterium oxalidis	83.1098	1005	1908	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	83.0235	1003	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_014199985.1	s__Methylobacterium rhodesianum	82.9984	1034	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_004348265.1	s__Methylobacterium segetis	82.9476	996	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697185.1	s__Methylobacterium brachiatum	82.8312	1103	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
GCF_003173715.1	s__Methylobacterium durans	82.7539	1042	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	82.7132	1013	1908	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	82.6292	1138	1908	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	82.6287	1108	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_000364445.2	s__Methylobacterium mesophilicum	82.3614	1085	1908	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	82.1488	1086	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_001423405.1	s__Methylobacterium sp001423405	81.966	937	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,731] [INFO] GTDB search result was written to GCF_902141845.1_CECT_9862_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:57,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:57,734] [INFO] DFAST_QC result json was written to GCF_902141845.1_CECT_9862_genomic.fna/dqc_result.json
[2024-01-24 13:29:57,734] [INFO] DFAST_QC completed!
[2024-01-24 13:29:57,735] [INFO] Total running time: 0h1m46s