[2023-06-07 19:37:28,699] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:37:28,701] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:37:28,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference
[2023-06-07 19:37:32,039] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:37:32,041] [INFO] Task started: Prodigal
[2023-06-07 19:37:32,041] [INFO] Running command: gunzip -c /var/lib/cwl/stg358a2c4b-85f1-46b1-a68b-9076ef897c52/GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna.gz | prodigal -d GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/cds.fna -a GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:37:42,796] [INFO] Task succeeded: Prodigal
[2023-06-07 19:37:42,797] [INFO] Task started: HMMsearch
[2023-06-07 19:37:42,797] [INFO] Running command: hmmsearch --tblout GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/reference_markers.hmm GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:37:43,025] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:37:43,026] [INFO] Found 6/6 markers.
[2023-06-07 19:37:43,053] [INFO] Query marker FASTA was written to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/markers.fasta
[2023-06-07 19:37:43,054] [INFO] Task started: Blastn
[2023-06-07 19:37:43,054] [INFO] Running command: blastn -query GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/markers.fasta -db /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/reference_markers.fasta -out GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:37:43,645] [INFO] Task succeeded: Blastn
[2023-06-07 19:37:43,649] [INFO] Selected 20 target genomes.
[2023-06-07 19:37:43,650] [INFO] Target genome list was writen to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/target_genomes.txt
[2023-06-07 19:37:43,654] [INFO] Task started: fastANI
[2023-06-07 19:37:43,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg358a2c4b-85f1-46b1-a68b-9076ef897c52/GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna.gz --refList GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/target_genomes.txt --output GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:37:55,508] [INFO] Task succeeded: fastANI
[2023-06-07 19:37:55,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:37:55,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:37:55,512] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:37:55,513] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:37:55,513] [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
--------------------------------------------------------------------------------
[2023-06-07 19:37:55,515] [INFO] DFAST Taxonomy check result was written to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/tc_result.tsv
[2023-06-07 19:37:55,515] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:37:55,515] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:37:55,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/checkm_data
[2023-06-07 19:37:55,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:37:55,546] [INFO] Task started: CheckM
[2023-06-07 19:37:55,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/checkm_input GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/checkm_result
[2023-06-07 19:38:31,118] [INFO] Task succeeded: CheckM
[2023-06-07 19:38:31,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:38:31,140] [INFO] ===== Completeness check finished =====
[2023-06-07 19:38:31,140] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:38:31,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/markers.fasta)
[2023-06-07 19:38:31,141] [INFO] Task started: Blastn
[2023-06-07 19:38:31,142] [INFO] Running command: blastn -query GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/markers.fasta -db /var/lib/cwl/stg9130978f-c4ca-4cf3-b68f-e7fd18ee3e42/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:38:32,013] [INFO] Task succeeded: Blastn
[2023-06-07 19:38:32,018] [INFO] Selected 20 target genomes.
[2023-06-07 19:38:32,018] [INFO] Target genome list was writen to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:38:32,026] [INFO] Task started: fastANI
[2023-06-07 19:38:32,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg358a2c4b-85f1-46b1-a68b-9076ef897c52/GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna.gz --refList GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/target_genomes_gtdb.txt --output GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:38:39,850] [INFO] Task succeeded: fastANI
[2023-06-07 19:38:39,858] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:38:39,858] [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_900316045.1	s__Cryptobacteroides sp900316045	99.5965	589	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.88	98.47	0.88	0.73	37	conclusive
GCA_002320605.1	s__Cryptobacteroides sp002320605	93.8701	527	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433355.1	s__Cryptobacteroides sp000433355	77.9173	102	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	77.6079	59	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_905235085.1	s__Cryptobacteroides sp905235085	77.4076	62	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	77.1201	68	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	77.1104	63	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	77.0289	88	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-07 19:38:39,860] [INFO] GTDB search result was written to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/result_gtdb.tsv
[2023-06-07 19:38:39,861] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:38:39,864] [INFO] DFAST_QC result json was written to GCA_902786145.1_Rumen_uncultured_genome_RUG13142_genomic.fna/dqc_result.json
[2023-06-07 19:38:39,864] [INFO] DFAST_QC completed!
[2023-06-07 19:38:39,864] [INFO] Total running time: 0h1m11s