[2023-06-08 14:28:03,411] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:03,415] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:03,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference
[2023-06-08 14:28:04,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:04,935] [INFO] Task started: Prodigal
[2023-06-08 14:28:04,935] [INFO] Running command: gunzip -c /var/lib/cwl/stgd498ee37-60c1-4a97-92d6-dacfb0c94fbb/GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna.gz | prodigal -d GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/cds.fna -a GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:16,672] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:16,672] [INFO] Task started: HMMsearch
[2023-06-08 14:28:16,672] [INFO] Running command: hmmsearch --tblout GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/reference_markers.hmm GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:16,928] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:16,930] [INFO] Found 6/6 markers.
[2023-06-08 14:28:16,953] [INFO] Query marker FASTA was written to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/markers.fasta
[2023-06-08 14:28:16,953] [INFO] Task started: Blastn
[2023-06-08 14:28:16,953] [INFO] Running command: blastn -query GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/markers.fasta -db /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/reference_markers.fasta -out GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:17,524] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:17,527] [INFO] Selected 20 target genomes.
[2023-06-08 14:28:17,528] [INFO] Target genome list was writen to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/target_genomes.txt
[2023-06-08 14:28:17,533] [INFO] Task started: fastANI
[2023-06-08 14:28:17,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgd498ee37-60c1-4a97-92d6-dacfb0c94fbb/GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna.gz --refList GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/target_genomes.txt --output GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:29,734] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:29,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:29,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:29,738] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:29,738] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:28:29,738] [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
--------------------------------------------------------------------------------
[2023-06-08 14:28:29,740] [INFO] DFAST Taxonomy check result was written to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/tc_result.tsv
[2023-06-08 14:28:29,741] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:29,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:29,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/checkm_data
[2023-06-08 14:28:29,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:29,773] [INFO] Task started: CheckM
[2023-06-08 14:28:29,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/checkm_input GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/checkm_result
[2023-06-08 14:29:07,788] [INFO] Task succeeded: CheckM
[2023-06-08 14:29:07,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:29:07,809] [INFO] ===== Completeness check finished =====
[2023-06-08 14:29:07,810] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:29:07,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/markers.fasta)
[2023-06-08 14:29:07,810] [INFO] Task started: Blastn
[2023-06-08 14:29:07,811] [INFO] Running command: blastn -query GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/markers.fasta -db /var/lib/cwl/stgf466b48d-c3f3-41e7-9b31-eb254634840f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:29:08,562] [INFO] Task succeeded: Blastn
[2023-06-08 14:29:08,567] [INFO] Selected 22 target genomes.
[2023-06-08 14:29:08,567] [INFO] Target genome list was writen to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:29:08,575] [INFO] Task started: fastANI
[2023-06-08 14:29:08,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgd498ee37-60c1-4a97-92d6-dacfb0c94fbb/GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna.gz --refList GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/target_genomes_gtdb.txt --output GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:17,451] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:17,463] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:29:17,463] [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	98.4703	598	678	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	94.001	575	678	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	77.8954	115	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.443	106	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	77.3158	97	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_002437305.1	s__Cryptobacteroides sp002437305	77.229	81	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.56	99.17	0.93	0.89	9	-
GCA_002314195.1	s__Cryptobacteroides sp002314195	77.1564	89	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.70	98.15	0.81	0.75	7	-
GCA_012522855.1	s__Cryptobacteroides sp012522855	76.9964	53	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	76.9194	72	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	76.8788	87	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	76.7363	73	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_018066065.1	s__Cryptobacteroides sp018066065	76.6597	53	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801205.1	s__Cryptobacteroides sp902801205	76.5099	56	678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.36	98.05	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:17,465] [INFO] GTDB search result was written to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:17,466] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:17,469] [INFO] DFAST_QC result json was written to GCA_902793355.1_Rumen_uncultured_genome_RUG13863_genomic.fna/dqc_result.json
[2023-06-08 14:29:17,469] [INFO] DFAST_QC completed!
[2023-06-08 14:29:17,469] [INFO] Total running time: 0h1m14s