[2023-06-05 18:59:28,027] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:59:28,029] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:59:28,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference
[2023-06-05 18:59:29,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:59:29,192] [INFO] Task started: Prodigal
[2023-06-05 18:59:29,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg139d9f44-0a11-4d3e-bc48-ea191cc8aed5/GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna.gz | prodigal -d GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/cds.fna -a GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:59:40,642] [INFO] Task succeeded: Prodigal
[2023-06-05 18:59:40,643] [INFO] Task started: HMMsearch
[2023-06-05 18:59:40,643] [INFO] Running command: hmmsearch --tblout GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/reference_markers.hmm GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:59:40,893] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:59:40,894] [INFO] Found 6/6 markers.
[2023-06-05 18:59:40,927] [INFO] Query marker FASTA was written to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/markers.fasta
[2023-06-05 18:59:40,928] [INFO] Task started: Blastn
[2023-06-05 18:59:40,928] [INFO] Running command: blastn -query GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/markers.fasta -db /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/reference_markers.fasta -out GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:41,520] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:41,525] [INFO] Selected 37 target genomes.
[2023-06-05 18:59:41,525] [INFO] Target genome list was writen to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/target_genomes.txt
[2023-06-05 18:59:41,533] [INFO] Task started: fastANI
[2023-06-05 18:59:41,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg139d9f44-0a11-4d3e-bc48-ea191cc8aed5/GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna.gz --refList GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/target_genomes.txt --output GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:00:07,148] [INFO] Task succeeded: fastANI
[2023-06-05 19:00:07,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:00:07,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:00:07,150] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:00:07,150] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 19:00:07,150] [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
--------------------------------------------------------------------------------
[2023-06-05 19:00:07,153] [INFO] DFAST Taxonomy check result was written to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/tc_result.tsv
[2023-06-05 19:00:07,153] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:00:07,153] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:00:07,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/checkm_data
[2023-06-05 19:00:07,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:00:07,180] [INFO] Task started: CheckM
[2023-06-05 19:00:07,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/checkm_input GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/checkm_result
[2023-06-05 19:00:42,570] [INFO] Task succeeded: CheckM
[2023-06-05 19:00:42,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:00:42,594] [INFO] ===== Completeness check finished =====
[2023-06-05 19:00:42,595] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:00:42,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/markers.fasta)
[2023-06-05 19:00:42,596] [INFO] Task started: Blastn
[2023-06-05 19:00:42,596] [INFO] Running command: blastn -query GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/markers.fasta -db /var/lib/cwl/stg1443ef2e-283d-4459-b888-d3265d7aaff1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:00:43,504] [INFO] Task succeeded: Blastn
[2023-06-05 19:00:43,510] [INFO] Selected 17 target genomes.
[2023-06-05 19:00:43,510] [INFO] Target genome list was writen to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:00:43,522] [INFO] Task started: fastANI
[2023-06-05 19:00:43,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg139d9f44-0a11-4d3e-bc48-ea191cc8aed5/GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna.gz --refList GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/target_genomes_gtdb.txt --output GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:00:51,318] [INFO] Task succeeded: fastANI
[2023-06-05 19:00:51,333] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:00:51,333] [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_900321655.1	s__Cryptobacteroides sp900321655	99.0013	515	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.46	96.30	0.88	0.86	12	conclusive
GCA_905235535.1	s__Cryptobacteroides sp905235535	84.4998	351	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316245.1	s__Cryptobacteroides sp900316245	83.5594	415	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.83	97.67	0.94	0.87	3	-
GCA_017423025.1	s__Cryptobacteroides sp017423025	83.4072	410	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373715.1	s__Cryptobacteroides sp002373715	83.3312	366	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.02	98.02	0.86	0.86	2	-
GCA_016285215.1	s__Cryptobacteroides sp016285215	83.3202	358	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617475.1	s__Cryptobacteroides sp017617475	83.0949	369	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794615.1	s__Cryptobacteroides sp902794615	82.2203	304	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	96.28	0.79	0.72	4	-
GCA_017480345.1	s__Cryptobacteroides sp017480345	82.1245	331	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.06	98.06	0.83	0.83	2	-
GCA_900317845.1	s__Cryptobacteroides sp900317845	81.2747	291	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.57	95.18	0.88	0.74	22	-
GCA_900318445.1	s__Cryptobacteroides sp900318445	80.8248	291	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.95	95.41	0.86	0.76	6	-
GCA_017509685.1	s__Cryptobacteroides sp017509685	80.658	306	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285175.1	s__Cryptobacteroides sp016285175	80.641	262	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447815.1	s__Cryptobacteroides sp017447815	80.525	298	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354005.1	s__Cryptobacteroides sp002354005	80.4561	245	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.47	96.01	0.76	0.69	14	-
GCA_900319405.1	s__Cryptobacteroides sp900319405	80.1506	294	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902788095.1	s__Cryptobacteroides sp902788095	80.0253	255	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	97.63	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-05 19:00:51,335] [INFO] GTDB search result was written to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/result_gtdb.tsv
[2023-06-05 19:00:51,336] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:00:51,339] [INFO] DFAST_QC result json was written to GCA_902784495.1_Rumen_uncultured_genome_RUG12972_genomic.fna/dqc_result.json
[2023-06-05 19:00:51,339] [INFO] DFAST_QC completed!
[2023-06-05 19:00:51,340] [INFO] Total running time: 0h1m23s