[2023-06-08 20:21:48,890] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:21:48,898] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:21:48,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference
[2023-06-08 20:21:50,356] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:21:50,357] [INFO] Task started: Prodigal
[2023-06-08 20:21:50,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b66bfda-cc9b-4e47-8875-dd2d7857a89c/GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna.gz | prodigal -d GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/cds.fna -a GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:22:01,330] [INFO] Task succeeded: Prodigal
[2023-06-08 20:22:01,331] [INFO] Task started: HMMsearch
[2023-06-08 20:22:01,331] [INFO] Running command: hmmsearch --tblout GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/reference_markers.hmm GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:22:01,619] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:22:01,620] [INFO] Found 6/6 markers.
[2023-06-08 20:22:01,657] [INFO] Query marker FASTA was written to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/markers.fasta
[2023-06-08 20:22:01,658] [INFO] Task started: Blastn
[2023-06-08 20:22:01,658] [INFO] Running command: blastn -query GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/markers.fasta -db /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/reference_markers.fasta -out GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:22:02,383] [INFO] Task succeeded: Blastn
[2023-06-08 20:22:02,388] [INFO] Selected 30 target genomes.
[2023-06-08 20:22:02,388] [INFO] Target genome list was writen to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/target_genomes.txt
[2023-06-08 20:22:02,390] [INFO] Task started: fastANI
[2023-06-08 20:22:02,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b66bfda-cc9b-4e47-8875-dd2d7857a89c/GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna.gz --refList GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/target_genomes.txt --output GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:22:24,529] [INFO] Task succeeded: fastANI
[2023-06-08 20:22:24,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:22:24,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:22:24,545] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:22:24,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:22:24,545] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.6987	59	1168	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.3701	60	1168	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.2869	57	1168	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	74.978	58	1168	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	74.9306	58	1168	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	74.9039	56	1168	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	74.8943	57	1168	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	74.7323	68	1168	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	74.7253	64	1168	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	74.6758	53	1168	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	74.6729	108	1168	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	74.6351	95	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:22:24,547] [INFO] DFAST Taxonomy check result was written to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/tc_result.tsv
[2023-06-08 20:22:24,548] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:22:24,548] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:22:24,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/checkm_data
[2023-06-08 20:22:24,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:22:24,591] [INFO] Task started: CheckM
[2023-06-08 20:22:24,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/checkm_input GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/checkm_result
[2023-06-08 20:22:59,011] [INFO] Task succeeded: CheckM
[2023-06-08 20:22:59,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:22:59,041] [INFO] ===== Completeness check finished =====
[2023-06-08 20:22:59,042] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:22:59,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/markers.fasta)
[2023-06-08 20:22:59,043] [INFO] Task started: Blastn
[2023-06-08 20:22:59,043] [INFO] Running command: blastn -query GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/markers.fasta -db /var/lib/cwl/stg2868fa96-48ce-466d-b183-a37e260b5f31/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:23:00,229] [INFO] Task succeeded: Blastn
[2023-06-08 20:23:00,234] [INFO] Selected 11 target genomes.
[2023-06-08 20:23:00,234] [INFO] Target genome list was writen to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:23:00,242] [INFO] Task started: fastANI
[2023-06-08 20:23:00,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b66bfda-cc9b-4e47-8875-dd2d7857a89c/GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna.gz --refList GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/target_genomes_gtdb.txt --output GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:23:10,596] [INFO] Task succeeded: fastANI
[2023-06-08 20:23:10,610] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:23:10,610] [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_902778995.1	s__UBA2862 sp902778995	100.0	1162	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017432405.1	s__UBA2862 sp017432405	85.0349	645	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765305.1	s__UBA2862 sp902765305	85.0324	671	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.39	97.59	0.81	0.77	4	-
GCA_017512905.1	s__UBA2862 sp017512905	84.8546	636	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.84	0.84	2	-
GCA_902798105.1	s__UBA2862 sp902798105	84.7241	629	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.82	0.82	2	-
GCA_900318045.1	s__UBA2862 sp900318045	84.4808	593	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.18	97.25	0.80	0.71	7	-
GCA_900317565.1	s__UBA2862 sp900317565	83.6394	557	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.55	99.55	0.85	0.85	2	-
GCA_902777335.1	s__UBA2862 sp902777335	82.8871	541	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:23:10,612] [INFO] GTDB search result was written to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/result_gtdb.tsv
[2023-06-08 20:23:10,613] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:23:10,616] [INFO] DFAST_QC result json was written to GCA_902778995.1_Rumen_uncultured_genome_RUG12424_genomic.fna/dqc_result.json
[2023-06-08 20:23:10,616] [INFO] DFAST_QC completed!
[2023-06-08 20:23:10,616] [INFO] Total running time: 0h1m22s