[2024-01-25 20:13:20,426] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference
[2024-01-25 20:13:21,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,559] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg55c01d77-a9a6-4b61-8b49-cc4e21df4ca5/GCF_017876165.1_ASM1787616v1_genomic.fna.gz | prodigal -d GCF_017876165.1_ASM1787616v1_genomic.fna/cds.fna -a GCF_017876165.1_ASM1787616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:40,209] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:40,209] [INFO] Task started: HMMsearch
[2024-01-25 20:13:40,210] [INFO] Running command: hmmsearch --tblout GCF_017876165.1_ASM1787616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/reference_markers.hmm GCF_017876165.1_ASM1787616v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:40,499] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:40,500] [INFO] Found 6/6 markers.
[2024-01-25 20:13:40,550] [INFO] Query marker FASTA was written to GCF_017876165.1_ASM1787616v1_genomic.fna/markers.fasta
[2024-01-25 20:13:40,550] [INFO] Task started: Blastn
[2024-01-25 20:13:40,550] [INFO] Running command: blastn -query GCF_017876165.1_ASM1787616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/reference_markers.fasta -out GCF_017876165.1_ASM1787616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:41,513] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:41,515] [INFO] Selected 12 target genomes.
[2024-01-25 20:13:41,516] [INFO] Target genome list was writen to GCF_017876165.1_ASM1787616v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:41,528] [INFO] Task started: fastANI
[2024-01-25 20:13:41,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c01d77-a9a6-4b61-8b49-cc4e21df4ca5/GCF_017876165.1_ASM1787616v1_genomic.fna.gz --refList GCF_017876165.1_ASM1787616v1_genomic.fna/target_genomes.txt --output GCF_017876165.1_ASM1787616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:01,160] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:01,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:01,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:01,169] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:01,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:01,170] [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
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	100.0	2233	2235	95	conclusive
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	85.7203	1446	2235	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	85.1846	1397	2235	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	85.1557	1386	2235	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	85.1181	1413	2235	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	85.1041	1342	2235	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	85.0963	1176	2235	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	85.0446	1392	2235	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	85.0004	1356	2235	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.8527	375	2235	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6239	405	2235	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.1371	247	2235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:01,171] [INFO] DFAST Taxonomy check result was written to GCF_017876165.1_ASM1787616v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:01,171] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:01,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:01,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/checkm_data
[2024-01-25 20:14:01,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:01,237] [INFO] Task started: CheckM
[2024-01-25 20:14:01,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876165.1_ASM1787616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876165.1_ASM1787616v1_genomic.fna/checkm_input GCF_017876165.1_ASM1787616v1_genomic.fna/checkm_result
[2024-01-25 20:15:01,267] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:01,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:01,288] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:01,288] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:01,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876165.1_ASM1787616v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:01,289] [INFO] Task started: Blastn
[2024-01-25 20:15:01,289] [INFO] Running command: blastn -query GCF_017876165.1_ASM1787616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg631b0f74-b31b-4c04-9b2d-ce09ac23193c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876165.1_ASM1787616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:03,233] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:03,236] [INFO] Selected 11 target genomes.
[2024-01-25 20:15:03,236] [INFO] Target genome list was writen to GCF_017876165.1_ASM1787616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:03,243] [INFO] Task started: fastANI
[2024-01-25 20:15:03,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c01d77-a9a6-4b61-8b49-cc4e21df4ca5/GCF_017876165.1_ASM1787616v1_genomic.fna.gz --refList GCF_017876165.1_ASM1787616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876165.1_ASM1787616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:22,511] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:22,518] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:22,519] [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_017876165.1	s__Azospirillum soli	100.0	2233	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876155.1	s__Azospirillum rugosum	85.6978	1449	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	85.4314	1397	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_008365375.1	s__Azospirillum sp008365375	85.2067	1348	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119195.2	s__Azospirillum baldaniorum	85.1765	1396	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_007827795.1	s__Azospirillum brasilense_E	85.1332	1346	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_007827815.1	s__Azospirillum brasilense_C	85.0996	1400	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	85.0703	1375	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315015.1	s__Azospirillum brasilense	85.0513	1375	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_002245955.1	s__Azospirillum brasilense_A	85.0284	1403	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	85.0004	1345	2235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:22,520] [INFO] GTDB search result was written to GCF_017876165.1_ASM1787616v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:22,520] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:22,523] [INFO] DFAST_QC result json was written to GCF_017876165.1_ASM1787616v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:22,523] [INFO] DFAST_QC completed!
[2024-01-25 20:15:22,523] [INFO] Total running time: 0h2m2s