[2023-06-08 18:46:12,025] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:46:12,045] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:46:12,045] [INFO] DQC Reference Directory: /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference
[2023-06-08 18:46:14,311] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:46:14,312] [INFO] Task started: Prodigal
[2023-06-08 18:46:14,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg12353ccd-4270-4a20-945d-f7f565ed9569/GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna.gz | prodigal -d GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/cds.fna -a GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:46:25,214] [INFO] Task succeeded: Prodigal
[2023-06-08 18:46:25,215] [INFO] Task started: HMMsearch
[2023-06-08 18:46:25,215] [INFO] Running command: hmmsearch --tblout GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/reference_markers.hmm GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:46:25,451] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:46:25,452] [INFO] Found 6/6 markers.
[2023-06-08 18:46:25,478] [INFO] Query marker FASTA was written to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/markers.fasta
[2023-06-08 18:46:25,478] [INFO] Task started: Blastn
[2023-06-08 18:46:25,478] [INFO] Running command: blastn -query GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/markers.fasta -db /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/reference_markers.fasta -out GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:46:26,079] [INFO] Task succeeded: Blastn
[2023-06-08 18:46:26,084] [INFO] Selected 30 target genomes.
[2023-06-08 18:46:26,085] [INFO] Target genome list was writen to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/target_genomes.txt
[2023-06-08 18:46:26,091] [INFO] Task started: fastANI
[2023-06-08 18:46:26,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg12353ccd-4270-4a20-945d-f7f565ed9569/GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna.gz --refList GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/target_genomes.txt --output GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:46:45,443] [INFO] Task succeeded: fastANI
[2023-06-08 18:46:45,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:46:45,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:46:45,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:46:45,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 18:46:45,447] [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 18:46:45,450] [INFO] DFAST Taxonomy check result was written to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/tc_result.tsv
[2023-06-08 18:46:45,451] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:46:45,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:46:45,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/checkm_data
[2023-06-08 18:46:45,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:46:45,481] [INFO] Task started: CheckM
[2023-06-08 18:46:45,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/checkm_input GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/checkm_result
[2023-06-08 18:47:20,438] [INFO] Task succeeded: CheckM
[2023-06-08 18:47:20,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:47:20,461] [INFO] ===== Completeness check finished =====
[2023-06-08 18:47:20,463] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:47:20,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/markers.fasta)
[2023-06-08 18:47:20,464] [INFO] Task started: Blastn
[2023-06-08 18:47:20,464] [INFO] Running command: blastn -query GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/markers.fasta -db /var/lib/cwl/stga56622a0-5829-4b32-a601-5e5105e12b10/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:47:21,293] [INFO] Task succeeded: Blastn
[2023-06-08 18:47:21,299] [INFO] Selected 26 target genomes.
[2023-06-08 18:47:21,299] [INFO] Target genome list was writen to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:47:21,312] [INFO] Task started: fastANI
[2023-06-08 18:47:21,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg12353ccd-4270-4a20-945d-f7f565ed9569/GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna.gz --refList GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/target_genomes_gtdb.txt --output GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:47:30,920] [INFO] Task succeeded: fastANI
[2023-06-08 18:47:30,938] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:47:30,938] [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_002472565.1	s__Cryptobacteroides sp002472565	99.3359	661	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.54	99.18	0.91	0.87	9	conclusive
GCA_900320185.1	s__Cryptobacteroides sp900320185	77.2817	66	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_900319855.1	s__Cryptobacteroides sp900319855	77.2083	70	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.81	0.89	0.84	6	-
GCA_004552115.1	s__Cryptobacteroides sp004552115	77.0413	62	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.49	98.12	0.74	0.72	3	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	76.998	77	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_002437305.1	s__Cryptobacteroides sp002437305	76.9603	60	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.56	99.17	0.93	0.89	9	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	76.9356	84	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	76.902	59	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_017427885.1	s__Cryptobacteroides sp017427885	76.8327	64	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	76.8247	70	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295455.1	s__Cryptobacteroides sp016295455	76.7092	60	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.79	98.71	0.83	0.82	3	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	76.6007	60	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_902766985.1	s__Cryptobacteroides sp902766985	76.571	56	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.09	97.97	0.82	0.68	3	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	76.4946	69	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017479265.1	s__Cryptobacteroides sp017479265	76.2011	66	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 18:47:30,940] [INFO] GTDB search result was written to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/result_gtdb.tsv
[2023-06-08 18:47:30,941] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:47:30,947] [INFO] DFAST_QC result json was written to GCA_902763075.1_Rumen_uncultured_genome_RUG10826_genomic.fna/dqc_result.json
[2023-06-08 18:47:30,948] [INFO] DFAST_QC completed!
[2023-06-08 18:47:30,948] [INFO] Total running time: 0h1m19s