[2023-06-16 19:45:03,166] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:45:03,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:45:03,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference
[2023-06-16 19:45:04,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:45:04,894] [INFO] Task started: Prodigal
[2023-06-16 19:45:04,894] [INFO] Running command: gunzip -c /var/lib/cwl/stge6a4293e-3b02-49d8-9bd7-9f706e6d42f3/GCA_009377495.1_ASM937749v1_genomic.fna.gz | prodigal -d GCA_009377495.1_ASM937749v1_genomic.fna/cds.fna -a GCA_009377495.1_ASM937749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:45:22,395] [INFO] Task succeeded: Prodigal
[2023-06-16 19:45:22,395] [INFO] Task started: HMMsearch
[2023-06-16 19:45:22,395] [INFO] Running command: hmmsearch --tblout GCA_009377495.1_ASM937749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/reference_markers.hmm GCA_009377495.1_ASM937749v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:45:22,730] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:45:22,731] [INFO] Found 6/6 markers.
[2023-06-16 19:45:22,776] [INFO] Query marker FASTA was written to GCA_009377495.1_ASM937749v1_genomic.fna/markers.fasta
[2023-06-16 19:45:22,776] [INFO] Task started: Blastn
[2023-06-16 19:45:22,776] [INFO] Running command: blastn -query GCA_009377495.1_ASM937749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/reference_markers.fasta -out GCA_009377495.1_ASM937749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:45:23,386] [INFO] Task succeeded: Blastn
[2023-06-16 19:45:23,390] [INFO] Selected 29 target genomes.
[2023-06-16 19:45:23,390] [INFO] Target genome list was writen to GCA_009377495.1_ASM937749v1_genomic.fna/target_genomes.txt
[2023-06-16 19:45:23,396] [INFO] Task started: fastANI
[2023-06-16 19:45:23,397] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a4293e-3b02-49d8-9bd7-9f706e6d42f3/GCA_009377495.1_ASM937749v1_genomic.fna.gz --refList GCA_009377495.1_ASM937749v1_genomic.fna/target_genomes.txt --output GCA_009377495.1_ASM937749v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:45:46,373] [INFO] Task succeeded: fastANI
[2023-06-16 19:45:46,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:45:46,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:45:46,381] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:45:46,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:45:46,382] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.8628	190	2124	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.8328	71	2124	95	below_threshold
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	74.8285	50	2124	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.7422	124	2124	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	74.729	60	2124	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	74.6774	74	2124	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	74.6732	68	2124	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.6678	95	2124	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.6633	97	2124	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.6235	113	2124	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:45:46,383] [INFO] DFAST Taxonomy check result was written to GCA_009377495.1_ASM937749v1_genomic.fna/tc_result.tsv
[2023-06-16 19:45:46,384] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:45:46,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:45:46,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/checkm_data
[2023-06-16 19:45:46,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:45:46,445] [INFO] Task started: CheckM
[2023-06-16 19:45:46,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009377495.1_ASM937749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009377495.1_ASM937749v1_genomic.fna/checkm_input GCA_009377495.1_ASM937749v1_genomic.fna/checkm_result
[2023-06-16 19:46:35,924] [INFO] Task succeeded: CheckM
[2023-06-16 19:46:35,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:46:35,944] [INFO] ===== Completeness check finished =====
[2023-06-16 19:46:35,944] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:46:35,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009377495.1_ASM937749v1_genomic.fna/markers.fasta)
[2023-06-16 19:46:35,945] [INFO] Task started: Blastn
[2023-06-16 19:46:35,945] [INFO] Running command: blastn -query GCA_009377495.1_ASM937749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4993f6e-690f-4c7b-8f9d-6f122e61d9b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_009377495.1_ASM937749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:46:36,773] [INFO] Task succeeded: Blastn
[2023-06-16 19:46:36,776] [INFO] Selected 18 target genomes.
[2023-06-16 19:46:36,776] [INFO] Target genome list was writen to GCA_009377495.1_ASM937749v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:46:36,779] [INFO] Task started: fastANI
[2023-06-16 19:46:36,780] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a4293e-3b02-49d8-9bd7-9f706e6d42f3/GCA_009377495.1_ASM937749v1_genomic.fna.gz --refList GCA_009377495.1_ASM937749v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009377495.1_ASM937749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:46:56,460] [INFO] Task succeeded: fastANI
[2023-06-16 19:46:56,472] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:46:56,472] [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_009377495.1	s__WHTT01 sp009377495	100.0	2118	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__WHTT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009377605.1	s__WHTT01 sp009377605	80.2487	1024	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__WHTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	76.0537	89	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222635.1	s__Gp6-AA40 sp003222635	75.9975	127	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	98.94	98.94	0.87	0.87	2	-
GCA_016865485.1	s__Luteitalea sp016865485	75.9888	216	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242705.1	s__SCN-69-37 sp003242705	75.9818	125	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SCN-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222675.1	s__QHWT01 sp003222675	75.9716	169	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883185.1	s__FEN-299 sp017883185	75.9421	107	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__FEN-299	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464065.1	s__Luteitalea sp001464065	75.9286	188	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	75.9247	172	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_003170135.1	s__Fen-181 sp003170135	75.8965	111	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	75.8868	161	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	75.8763	167	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
GCF_001618865.1	s__Luteitalea pratensis	75.8623	188	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	75.7453	120	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	75.6298	125	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	75.5909	190	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016210935.1	s__JACQTH01 sp016210935	75.4484	70	2124	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JACQTH01;g__JACQTH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:46:56,474] [INFO] GTDB search result was written to GCA_009377495.1_ASM937749v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:46:56,474] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:46:56,477] [INFO] DFAST_QC result json was written to GCA_009377495.1_ASM937749v1_genomic.fna/dqc_result.json
[2023-06-16 19:46:56,478] [INFO] DFAST_QC completed!
[2023-06-16 19:46:56,478] [INFO] Total running time: 0h1m53s