[2023-06-13 12:28:00,652] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:28:00,655] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:28:00,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference
[2023-06-13 12:28:02,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:28:02,518] [INFO] Task started: Prodigal
[2023-06-13 12:28:02,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgefef5f22-cb5c-46bf-8209-c09dae5d542d/GCA_022574385.1_ASM2257438v1_genomic.fna.gz | prodigal -d GCA_022574385.1_ASM2257438v1_genomic.fna/cds.fna -a GCA_022574385.1_ASM2257438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:28:06,423] [INFO] Task succeeded: Prodigal
[2023-06-13 12:28:06,423] [INFO] Task started: HMMsearch
[2023-06-13 12:28:06,423] [INFO] Running command: hmmsearch --tblout GCA_022574385.1_ASM2257438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/reference_markers.hmm GCA_022574385.1_ASM2257438v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:28:06,616] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:28:06,617] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgefef5f22-cb5c-46bf-8209-c09dae5d542d/GCA_022574385.1_ASM2257438v1_genomic.fna.gz]
[2023-06-13 12:28:06,639] [INFO] Query marker FASTA was written to GCA_022574385.1_ASM2257438v1_genomic.fna/markers.fasta
[2023-06-13 12:28:06,640] [INFO] Task started: Blastn
[2023-06-13 12:28:06,640] [INFO] Running command: blastn -query GCA_022574385.1_ASM2257438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/reference_markers.fasta -out GCA_022574385.1_ASM2257438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:07,372] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:07,376] [INFO] Selected 16 target genomes.
[2023-06-13 12:28:07,376] [INFO] Target genome list was writen to GCA_022574385.1_ASM2257438v1_genomic.fna/target_genomes.txt
[2023-06-13 12:28:07,378] [INFO] Task started: fastANI
[2023-06-13 12:28:07,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgefef5f22-cb5c-46bf-8209-c09dae5d542d/GCA_022574385.1_ASM2257438v1_genomic.fna.gz --refList GCA_022574385.1_ASM2257438v1_genomic.fna/target_genomes.txt --output GCA_022574385.1_ASM2257438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:28:24,053] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:24,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:28:24,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:28:24,067] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:28:24,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 12:28:24,068] [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
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.8748	59	279	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.8658	63	279	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.8275	64	279	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	76.7903	65	279	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.7269	83	279	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.7065	80	279	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.6167	64	279	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.4529	77	279	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.4214	67	279	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.4071	76	279	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.1735	104	279	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1516	95	279	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1394	96	279	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.9312	67	279	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:28:24,077] [INFO] DFAST Taxonomy check result was written to GCA_022574385.1_ASM2257438v1_genomic.fna/tc_result.tsv
[2023-06-13 12:28:24,080] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:28:24,080] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:28:24,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/checkm_data
[2023-06-13 12:28:24,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:28:24,102] [INFO] Task started: CheckM
[2023-06-13 12:28:24,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022574385.1_ASM2257438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022574385.1_ASM2257438v1_genomic.fna/checkm_input GCA_022574385.1_ASM2257438v1_genomic.fna/checkm_result
[2023-06-13 12:28:43,146] [INFO] Task succeeded: CheckM
[2023-06-13 12:28:43,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.11%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 12:28:43,183] [INFO] ===== Completeness check finished =====
[2023-06-13 12:28:43,184] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:28:43,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022574385.1_ASM2257438v1_genomic.fna/markers.fasta)
[2023-06-13 12:28:43,185] [INFO] Task started: Blastn
[2023-06-13 12:28:43,185] [INFO] Running command: blastn -query GCA_022574385.1_ASM2257438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg243faa2a-fc73-4d57-88fb-e7307211d38d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022574385.1_ASM2257438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:44,231] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:44,236] [INFO] Selected 15 target genomes.
[2023-06-13 12:28:44,237] [INFO] Target genome list was writen to GCA_022574385.1_ASM2257438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:28:44,243] [INFO] Task started: fastANI
[2023-06-13 12:28:44,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgefef5f22-cb5c-46bf-8209-c09dae5d542d/GCA_022574385.1_ASM2257438v1_genomic.fna.gz --refList GCA_022574385.1_ASM2257438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022574385.1_ASM2257438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:28:53,361] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:53,381] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 12:28:53,381] [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
GCA_002938075.1	s__Casp-alpha2 sp002938075	78.1422	75	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.8255	103	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_013349695.1	s__GCA-2686765 sp013349695	77.6416	69	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.5526	91	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	77.5045	85	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.2102	90	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	76.9935	54	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	76.9362	71	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.8268	73	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	76.4971	77	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.4342	69	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_006739055.1	s__Stella vacuolata	76.2589	82	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869675.1	s__VGDP01 sp016869675	76.051	57	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__VGDP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:28:53,384] [INFO] GTDB search result was written to GCA_022574385.1_ASM2257438v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:28:53,385] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:28:53,389] [INFO] DFAST_QC result json was written to GCA_022574385.1_ASM2257438v1_genomic.fna/dqc_result.json
[2023-06-13 12:28:53,390] [INFO] DFAST_QC completed!
[2023-06-13 12:28:53,390] [INFO] Total running time: 0h0m53s