[2023-06-04 19:38:30,607] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:30,613] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:30,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference
[2023-06-04 19:38:33,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:33,123] [INFO] Task started: Prodigal
[2023-06-04 19:38:33,124] [INFO] Running command: gunzip -c /var/lib/cwl/stge657cab9-1c68-4e0a-aecc-1a11bd2f5287/GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna.gz | prodigal -d GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/cds.fna -a GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:37,544] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:37,545] [INFO] Task started: HMMsearch
[2023-06-04 19:38:37,545] [INFO] Running command: hmmsearch --tblout GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/reference_markers.hmm GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:37,784] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:37,786] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge657cab9-1c68-4e0a-aecc-1a11bd2f5287/GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna.gz]
[2023-06-04 19:38:37,809] [INFO] Query marker FASTA was written to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/markers.fasta
[2023-06-04 19:38:37,810] [INFO] Task started: Blastn
[2023-06-04 19:38:37,810] [INFO] Running command: blastn -query GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/reference_markers.fasta -out GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:38,493] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:38,497] [INFO] Selected 29 target genomes.
[2023-06-04 19:38:38,498] [INFO] Target genome list was writen to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/target_genomes.txt
[2023-06-04 19:38:38,501] [INFO] Task started: fastANI
[2023-06-04 19:38:38,502] [INFO] Running command: fastANI --query /var/lib/cwl/stge657cab9-1c68-4e0a-aecc-1a11bd2f5287/GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna.gz --refList GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/target_genomes.txt --output GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:52,211] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:52,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:52,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:52,229] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:52,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 19:38:52,230] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.9857	67	568	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.9435	67	568	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.8978	64	568	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.8248	63	568	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8209	70	568	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.7249	62	568	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.6652	72	568	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.3031	52	568	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.2183	50	568	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:38:52,232] [INFO] DFAST Taxonomy check result was written to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/tc_result.tsv
[2023-06-04 19:38:52,232] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:52,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:52,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/checkm_data
[2023-06-04 19:38:52,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:52,261] [INFO] Task started: CheckM
[2023-06-04 19:38:52,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/checkm_input GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/checkm_result
[2023-06-04 19:39:12,326] [INFO] Task succeeded: CheckM
[2023-06-04 19:39:12,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.31%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-04 19:39:12,358] [INFO] ===== Completeness check finished =====
[2023-06-04 19:39:12,358] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:39:12,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/markers.fasta)
[2023-06-04 19:39:12,359] [INFO] Task started: Blastn
[2023-06-04 19:39:12,359] [INFO] Running command: blastn -query GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/markers.fasta -db /var/lib/cwl/stg09c90ffa-2ef7-4e11-9b8f-3c455b752ac5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:39:13,501] [INFO] Task succeeded: Blastn
[2023-06-04 19:39:13,506] [INFO] Selected 15 target genomes.
[2023-06-04 19:39:13,506] [INFO] Target genome list was writen to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:39:13,572] [INFO] Task started: fastANI
[2023-06-04 19:39:13,572] [INFO] Running command: fastANI --query /var/lib/cwl/stge657cab9-1c68-4e0a-aecc-1a11bd2f5287/GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna.gz --refList GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/target_genomes_gtdb.txt --output GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:39:20,281] [INFO] Task succeeded: fastANI
[2023-06-04 19:39:20,293] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:39:20,294] [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_900315595.1	s__Faecousia sp900315595	97.4836	496	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.62	97.05	0.87	0.79	33	conclusive
GCA_017425545.1	s__Faecousia sp017425545	82.6604	214	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767915.1	s__Faecousia sp902767915	80.5967	249	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.86	97.78	0.84	0.82	3	-
GCA_017519005.1	s__Faecousia sp017519005	80.4768	262	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.84	97.84	0.75	0.75	2	-
GCA_016292255.1	s__Faecousia sp016292255	80.3754	260	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541995.1	s__Faecousia sp017541995	80.2604	271	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540945.1	s__Faecousia sp017540945	80.2404	246	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.32	98.32	0.76	0.76	2	-
GCA_902795195.1	s__Faecousia sp902795195	79.8068	199	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	77.13	90	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395905.1	s__Avoscillospira_A sp904395905	76.6886	82	568	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:39:20,296] [INFO] GTDB search result was written to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/result_gtdb.tsv
[2023-06-04 19:39:20,296] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:39:20,300] [INFO] DFAST_QC result json was written to GCA_902767755.1_Rumen_uncultured_genome_RUG11292_genomic.fna/dqc_result.json
[2023-06-04 19:39:20,300] [INFO] DFAST_QC completed!
[2023-06-04 19:39:20,300] [INFO] Total running time: 0h0m50s