[2023-06-04 23:48:11,096] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:48:11,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:48:11,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference
[2023-06-04 23:48:12,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:48:12,946] [INFO] Task started: Prodigal
[2023-06-04 23:48:12,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cdb7169-234a-446b-98a5-9dae2f7865f1/GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna.gz | prodigal -d GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/cds.fna -a GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:48:19,977] [INFO] Task succeeded: Prodigal
[2023-06-04 23:48:19,977] [INFO] Task started: HMMsearch
[2023-06-04 23:48:19,977] [INFO] Running command: hmmsearch --tblout GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/reference_markers.hmm GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:48:20,228] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:48:20,229] [INFO] Found 6/6 markers.
[2023-06-04 23:48:20,254] [INFO] Query marker FASTA was written to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/markers.fasta
[2023-06-04 23:48:20,254] [INFO] Task started: Blastn
[2023-06-04 23:48:20,254] [INFO] Running command: blastn -query GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/markers.fasta -db /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/reference_markers.fasta -out GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:20,837] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:20,843] [INFO] Selected 17 target genomes.
[2023-06-04 23:48:20,843] [INFO] Target genome list was writen to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/target_genomes.txt
[2023-06-04 23:48:20,850] [INFO] Task started: fastANI
[2023-06-04 23:48:20,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdb7169-234a-446b-98a5-9dae2f7865f1/GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna.gz --refList GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/target_genomes.txt --output GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:48:32,520] [INFO] Task succeeded: fastANI
[2023-06-04 23:48:32,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:48:32,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:48:32,536] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:48:32,536] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:48:32,537] [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
--------------------------------------------------------------------------------
[2023-06-04 23:48:32,546] [INFO] DFAST Taxonomy check result was written to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/tc_result.tsv
[2023-06-04 23:48:32,547] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:48:32,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:48:32,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/checkm_data
[2023-06-04 23:48:32,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:48:32,581] [INFO] Task started: CheckM
[2023-06-04 23:48:32,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/checkm_input GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/checkm_result
[2023-06-04 23:48:59,117] [INFO] Task succeeded: CheckM
[2023-06-04 23:48:59,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 23:48:59,141] [INFO] ===== Completeness check finished =====
[2023-06-04 23:48:59,141] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:48:59,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/markers.fasta)
[2023-06-04 23:48:59,142] [INFO] Task started: Blastn
[2023-06-04 23:48:59,142] [INFO] Running command: blastn -query GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/markers.fasta -db /var/lib/cwl/stg15b2097b-c9f4-48f6-9561-51ca6452e244/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:59,901] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:59,907] [INFO] Selected 8 target genomes.
[2023-06-04 23:48:59,907] [INFO] Target genome list was writen to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:48:59,914] [INFO] Task started: fastANI
[2023-06-04 23:48:59,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdb7169-234a-446b-98a5-9dae2f7865f1/GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna.gz --refList GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/target_genomes_gtdb.txt --output GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:49:05,011] [INFO] Task succeeded: fastANI
[2023-06-04 23:49:05,022] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:49:05,022] [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_900316905.1	s__Treponema_D sp900316905	96.719	660	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.02	96.19	0.87	0.83	16	conclusive
GCA_002391235.1	s__Treponema_D sp002391235	88.5791	561	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799665.1	s__Treponema_D sp902799665	88.5619	584	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.67	96.44	0.88	0.84	3	-
GCA_902792795.1	s__Treponema_D sp902792795	87.0677	568	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.12	97.12	0.85	0.85	2	-
GCA_902799965.1	s__Treponema_D sp902799965	86.1212	536	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290995.1	s__Treponema_D sp016290995	85.8871	555	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645785.1	s__Treponema_D sp017645785	85.6214	560	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551705.1	s__Treponema_D sp017551705	83.39	529	800	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:49:05,024] [INFO] GTDB search result was written to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/result_gtdb.tsv
[2023-06-04 23:49:05,025] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:49:05,027] [INFO] DFAST_QC result json was written to GCA_902792365.1_Rumen_uncultured_genome_RUG13769_genomic.fna/dqc_result.json
[2023-06-04 23:49:05,028] [INFO] DFAST_QC completed!
[2023-06-04 23:49:05,028] [INFO] Total running time: 0h0m54s