[2023-06-05 13:10:33,546] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:10:33,549] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:10:33,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference
[2023-06-05 13:10:35,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:10:35,774] [INFO] Task started: Prodigal
[2023-06-05 13:10:35,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcea20fb-f8ad-4e70-a404-f3e344b35b8d/GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna.gz | prodigal -d GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/cds.fna -a GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:10:46,465] [INFO] Task succeeded: Prodigal
[2023-06-05 13:10:46,465] [INFO] Task started: HMMsearch
[2023-06-05 13:10:46,465] [INFO] Running command: hmmsearch --tblout GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/reference_markers.hmm GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:10:46,644] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:10:46,645] [INFO] Found 6/6 markers.
[2023-06-05 13:10:46,665] [INFO] Query marker FASTA was written to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/markers.fasta
[2023-06-05 13:10:46,665] [INFO] Task started: Blastn
[2023-06-05 13:10:46,665] [INFO] Running command: blastn -query GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/reference_markers.fasta -out GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:10:47,272] [INFO] Task succeeded: Blastn
[2023-06-05 13:10:47,285] [INFO] Selected 21 target genomes.
[2023-06-05 13:10:47,286] [INFO] Target genome list was writen to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/target_genomes.txt
[2023-06-05 13:10:47,286] [INFO] Task started: fastANI
[2023-06-05 13:10:47,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcea20fb-f8ad-4e70-a404-f3e344b35b8d/GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna.gz --refList GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/target_genomes.txt --output GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:10:58,229] [INFO] Task succeeded: fastANI
[2023-06-05 13:10:58,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:10:58,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:10:58,241] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:10:58,241] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:10:58,241] [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
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	76.6646	53	590	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.4976	67	590	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	76.4913	54	590	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.4812	69	590	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	76.4025	57	590	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.3852	57	590	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.2968	66	590	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.2927	65	590	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.2849	65	590	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.267	66	590	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	76.1857	52	590	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.0276	55	590	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:10:58,243] [INFO] DFAST Taxonomy check result was written to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/tc_result.tsv
[2023-06-05 13:10:58,244] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:10:58,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:10:58,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/checkm_data
[2023-06-05 13:10:58,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:10:58,267] [INFO] Task started: CheckM
[2023-06-05 13:10:58,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/checkm_input GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/checkm_result
[2023-06-05 13:11:31,147] [INFO] Task succeeded: CheckM
[2023-06-05 13:11:31,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:11:31,166] [INFO] ===== Completeness check finished =====
[2023-06-05 13:11:31,166] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:11:31,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/markers.fasta)
[2023-06-05 13:11:31,167] [INFO] Task started: Blastn
[2023-06-05 13:11:31,167] [INFO] Running command: blastn -query GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaf1dbb4-da8f-4a94-abe6-d0b7878921bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:11:32,110] [INFO] Task succeeded: Blastn
[2023-06-05 13:11:32,113] [INFO] Selected 8 target genomes.
[2023-06-05 13:11:32,114] [INFO] Target genome list was writen to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:11:32,117] [INFO] Task started: fastANI
[2023-06-05 13:11:32,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcea20fb-f8ad-4e70-a404-f3e344b35b8d/GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna.gz --refList GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/target_genomes_gtdb.txt --output GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:11:36,147] [INFO] Task succeeded: fastANI
[2023-06-05 13:11:36,155] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:11:36,155] [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_902784965.1	s__Bact-11 sp902784965	100.0	587	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905233345.1	s__Bact-11 sp905233345	85.48	441	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290385.1	s__Bact-11 sp016290385	85.3755	407	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447265.1	s__Bact-11 sp017447265	84.9482	382	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619655.1	s__Bact-11 sp017619655	84.3907	283	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361615.1	s__Bact-11 sp002361615	82.5486	382	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.07	96.21	0.85	0.79	8	-
GCA_902778855.1	s__Bact-11 sp902778855	82.4837	368	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.53	96.67	0.88	0.85	8	-
GCA_902789445.1	s__Bact-11 sp902789445	82.3206	339	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.70	97.46	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-05 13:11:36,157] [INFO] GTDB search result was written to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/result_gtdb.tsv
[2023-06-05 13:11:36,157] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:11:36,161] [INFO] DFAST_QC result json was written to GCA_902784965.1_Rumen_uncultured_genome_RUG13016_genomic.fna/dqc_result.json
[2023-06-05 13:11:36,161] [INFO] DFAST_QC completed!
[2023-06-05 13:11:36,161] [INFO] Total running time: 0h1m3s