[2023-06-12 23:28:19,255] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:28:19,260] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:28:19,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference
[2023-06-12 23:28:20,629] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:28:20,630] [INFO] Task started: Prodigal
[2023-06-12 23:28:20,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg207169c9-4ce7-4546-b91d-b0fd48cf7c0f/GCA_022796255.1_ASM2279625v1_genomic.fna.gz | prodigal -d GCA_022796255.1_ASM2279625v1_genomic.fna/cds.fna -a GCA_022796255.1_ASM2279625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:28:29,597] [INFO] Task succeeded: Prodigal
[2023-06-12 23:28:29,598] [INFO] Task started: HMMsearch
[2023-06-12 23:28:29,598] [INFO] Running command: hmmsearch --tblout GCA_022796255.1_ASM2279625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/reference_markers.hmm GCA_022796255.1_ASM2279625v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:28:29,869] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:28:29,870] [INFO] Found 6/6 markers.
[2023-06-12 23:28:29,907] [INFO] Query marker FASTA was written to GCA_022796255.1_ASM2279625v1_genomic.fna/markers.fasta
[2023-06-12 23:28:29,908] [INFO] Task started: Blastn
[2023-06-12 23:28:29,908] [INFO] Running command: blastn -query GCA_022796255.1_ASM2279625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/reference_markers.fasta -out GCA_022796255.1_ASM2279625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:28:30,536] [INFO] Task succeeded: Blastn
[2023-06-12 23:28:30,541] [INFO] Selected 24 target genomes.
[2023-06-12 23:28:30,541] [INFO] Target genome list was writen to GCA_022796255.1_ASM2279625v1_genomic.fna/target_genomes.txt
[2023-06-12 23:28:30,545] [INFO] Task started: fastANI
[2023-06-12 23:28:30,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg207169c9-4ce7-4546-b91d-b0fd48cf7c0f/GCA_022796255.1_ASM2279625v1_genomic.fna.gz --refList GCA_022796255.1_ASM2279625v1_genomic.fna/target_genomes.txt --output GCA_022796255.1_ASM2279625v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:28:46,671] [INFO] Task succeeded: fastANI
[2023-06-12 23:28:46,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:28:46,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:28:46,684] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:28:46,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:28:46,684] [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
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.9775	150	1182	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.9561	153	1182	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2801	93	1182	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.2194	105	1182	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.1435	106	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:28:46,687] [INFO] DFAST Taxonomy check result was written to GCA_022796255.1_ASM2279625v1_genomic.fna/tc_result.tsv
[2023-06-12 23:28:46,688] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:28:46,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:28:46,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/checkm_data
[2023-06-12 23:28:46,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:28:46,727] [INFO] Task started: CheckM
[2023-06-12 23:28:46,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022796255.1_ASM2279625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022796255.1_ASM2279625v1_genomic.fna/checkm_input GCA_022796255.1_ASM2279625v1_genomic.fna/checkm_result
[2023-06-12 23:29:18,132] [INFO] Task succeeded: CheckM
[2023-06-12 23:29:18,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:29:18,157] [INFO] ===== Completeness check finished =====
[2023-06-12 23:29:18,157] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:29:18,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022796255.1_ASM2279625v1_genomic.fna/markers.fasta)
[2023-06-12 23:29:18,158] [INFO] Task started: Blastn
[2023-06-12 23:29:18,158] [INFO] Running command: blastn -query GCA_022796255.1_ASM2279625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb22e4ef5-88ba-4e9f-a33f-da4487c2f417/dqc_reference/reference_markers_gtdb.fasta -out GCA_022796255.1_ASM2279625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:29:19,199] [INFO] Task succeeded: Blastn
[2023-06-12 23:29:19,205] [INFO] Selected 13 target genomes.
[2023-06-12 23:29:19,205] [INFO] Target genome list was writen to GCA_022796255.1_ASM2279625v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:29:19,213] [INFO] Task started: fastANI
[2023-06-12 23:29:19,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg207169c9-4ce7-4546-b91d-b0fd48cf7c0f/GCA_022796255.1_ASM2279625v1_genomic.fna.gz --refList GCA_022796255.1_ASM2279625v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022796255.1_ASM2279625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:29:27,952] [INFO] Task succeeded: fastANI
[2023-06-12 23:29:27,971] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:29:27,972] [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_011958945.1	s__Kineothrix sp011958945	98.4785	898	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	98.22	97.96	0.71	0.68	3	conclusive
GCA_009911195.1	s__Kineothrix sp009911195	83.9493	820	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588855.1	s__Kineothrix sp910588855	78.6516	395	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576535.1	s__Kineothrix sp910576535	78.6477	369	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403275.2	s__Kineothrix sp000403275	78.3936	366	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	98.66	98.53	0.88	0.87	4	-
GCA_003488965.1	s__Kineothrix sp003488965	78.346	253	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585965.1	s__Kineothrix sp910585965	78.2419	383	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579935.1	s__Kineothrix sp910579935	77.3393	241	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586275.1	s__Kineothrix sp910586275	77.3044	216	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578405.1	s__Kineothrix sp910578405	76.919	227	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804655.1	s__UBA3282 sp014804655	76.6031	76	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465845.1	s__Acetatifactor sp017465845	76.058	60	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056915.1	s__Acetatifactor sp015056915	75.7374	61	1182	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:29:27,974] [INFO] GTDB search result was written to GCA_022796255.1_ASM2279625v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:29:27,974] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:29:27,979] [INFO] DFAST_QC result json was written to GCA_022796255.1_ASM2279625v1_genomic.fna/dqc_result.json
[2023-06-12 23:29:27,979] [INFO] DFAST_QC completed!
[2023-06-12 23:29:27,980] [INFO] Total running time: 0h1m9s