[2024-01-24 12:30:48,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference
[2024-01-24 12:30:49,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:49,905] [INFO] Task started: Prodigal
[2024-01-24 12:30:49,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg8420cef5-b183-4b36-86d6-e28442c59871/GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna.gz | prodigal -d GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/cds.fna -a GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:07,697] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:07,697] [INFO] Task started: HMMsearch
[2024-01-24 12:31:07,698] [INFO] Running command: hmmsearch --tblout GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/reference_markers.hmm GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:07,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:07,996] [INFO] Found 6/6 markers.
[2024-01-24 12:31:08,028] [INFO] Query marker FASTA was written to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/markers.fasta
[2024-01-24 12:31:08,029] [INFO] Task started: Blastn
[2024-01-24 12:31:08,029] [INFO] Running command: blastn -query GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/reference_markers.fasta -out GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,621] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,624] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:08,624] [INFO] Target genome list was writen to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:08,635] [INFO] Task started: fastANI
[2024-01-24 12:31:08,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg8420cef5-b183-4b36-86d6-e28442c59871/GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna.gz --refList GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/target_genomes.txt --output GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:24,025] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:24,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:24,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:24,039] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:24,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:24,040] [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
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	99.9999	1144	1145	95	conclusive
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	83.2071	60	1145	95	below_threshold
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	81.5638	97	1145	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	80.1848	316	1145	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	77.3372	72	1145	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	77.3077	72	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,042] [INFO] DFAST Taxonomy check result was written to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:24,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:24,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:24,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/checkm_data
[2024-01-24 12:31:24,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:24,084] [INFO] Task started: CheckM
[2024-01-24 12:31:24,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/checkm_input GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/checkm_result
[2024-01-24 12:32:15,704] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:15,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:15,731] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:15,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:15,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/markers.fasta)
[2024-01-24 12:32:15,732] [INFO] Task started: Blastn
[2024-01-24 12:32:15,732] [INFO] Running command: blastn -query GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b56337-36e4-4353-9178-5ff69db68907/dqc_reference/reference_markers_gtdb.fasta -out GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:16,518] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:16,522] [INFO] Selected 19 target genomes.
[2024-01-24 12:32:16,522] [INFO] Target genome list was writen to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:16,582] [INFO] Task started: fastANI
[2024-01-24 12:32:16,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg8420cef5-b183-4b36-86d6-e28442c59871/GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna.gz --refList GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:27,118] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:27,126] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:27,126] [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
GCF_000296465.1	s__Barnesiella intestinihominis	99.9999	1144	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	conclusive
GCF_000512915.1	s__Barnesiella viscericola	80.2215	317	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.37	97.37	0.91	0.91	2	-
GCF_002159975.1	s__Barnesiella merdigallinarum	79.787	335	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.77	95.24	0.93	0.91	5	-
GCA_019114445.1	s__Barnesiella excrementigallinarum	79.5904	415	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161555.1	s__Barnesiella merdipullorum	79.0473	318	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	99.43	99.43	0.98	0.98	2	-
GCA_019115485.1	s__Barnesiella excrementavium	78.5852	291	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541965.1	s__Parabacteroides sp900541965	77.0478	53	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.98	99.95	0.94	0.89	3	-
GCA_017462265.1	s__UBA11471 sp017462265	76.4149	53	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,128] [INFO] GTDB search result was written to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:27,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:27,131] [INFO] DFAST_QC result json was written to GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna/dqc_result.json
[2024-01-24 12:32:27,131] [INFO] DFAST_QC completed!
[2024-01-24 12:32:27,131] [INFO] Total running time: 0h1m39s