[2023-06-08 14:28:06,364] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:06,367] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:06,367] [INFO] DQC Reference Directory: /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference
[2023-06-08 14:28:08,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:08,027] [INFO] Task started: Prodigal
[2023-06-08 14:28:08,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg62c2f1e8-9b6f-47ff-8bb7-2b1eb46d93ef/GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna.gz | prodigal -d GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/cds.fna -a GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:22,112] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:22,112] [INFO] Task started: HMMsearch
[2023-06-08 14:28:22,112] [INFO] Running command: hmmsearch --tblout GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/reference_markers.hmm GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:22,389] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:22,391] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62c2f1e8-9b6f-47ff-8bb7-2b1eb46d93ef/GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna.gz]
[2023-06-08 14:28:22,418] [INFO] Query marker FASTA was written to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/markers.fasta
[2023-06-08 14:28:22,418] [INFO] Task started: Blastn
[2023-06-08 14:28:22,419] [INFO] Running command: blastn -query GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/reference_markers.fasta -out GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:23,035] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:23,058] [INFO] Selected 20 target genomes.
[2023-06-08 14:28:23,059] [INFO] Target genome list was writen to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/target_genomes.txt
[2023-06-08 14:28:23,060] [INFO] Task started: fastANI
[2023-06-08 14:28:23,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg62c2f1e8-9b6f-47ff-8bb7-2b1eb46d93ef/GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna.gz --refList GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/target_genomes.txt --output GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:34,980] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:34,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:34,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:34,987] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:34,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:28:34,988] [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
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.9483	50	803	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.8159	52	803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:28:34,990] [INFO] DFAST Taxonomy check result was written to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/tc_result.tsv
[2023-06-08 14:28:34,991] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:34,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:34,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/checkm_data
[2023-06-08 14:28:34,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:35,026] [INFO] Task started: CheckM
[2023-06-08 14:28:35,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/checkm_input GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/checkm_result
[2023-06-08 14:29:16,749] [INFO] Task succeeded: CheckM
[2023-06-08 14:29:16,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:29:16,767] [INFO] ===== Completeness check finished =====
[2023-06-08 14:29:16,767] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:29:16,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/markers.fasta)
[2023-06-08 14:29:16,768] [INFO] Task started: Blastn
[2023-06-08 14:29:16,768] [INFO] Running command: blastn -query GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e8f33e-a064-4976-9975-484c5f3b2438/dqc_reference/reference_markers_gtdb.fasta -out GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:29:17,531] [INFO] Task succeeded: Blastn
[2023-06-08 14:29:17,536] [INFO] Selected 24 target genomes.
[2023-06-08 14:29:17,537] [INFO] Target genome list was writen to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:29:17,555] [INFO] Task started: fastANI
[2023-06-08 14:29:17,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg62c2f1e8-9b6f-47ff-8bb7-2b1eb46d93ef/GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna.gz --refList GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/target_genomes_gtdb.txt --output GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:27,795] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:27,808] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:29:27,809] [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_900314335.1	s__UBA6398 sp900314335	100.0	789	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6398	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_900772575.1	s__Alloprevotella sp900772575	77.2177	56	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017445145.1	s__UBA4372 sp017445145	77.173	63	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792555.1	s__UBA6382 sp902792555	76.9601	66	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	96.62	96.42	0.86	0.84	6	-
GCA_905234605.1	s__UBA4372 sp905234605	76.6096	74	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017933995.1	s__Alloprevotella sp017933995	76.5916	82	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714085.1	s__Alloprevotella pullistercoris	76.4631	57	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017940565.1	s__UBA6382 sp017940565	76.308	57	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	98.65	98.65	0.88	0.88	2	-
GCA_004556745.1	s__Alloprevotella sp004556745	76.2458	68	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.07	96.01	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:27,811] [INFO] GTDB search result was written to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:27,811] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:27,814] [INFO] DFAST_QC result json was written to GCA_902803875.1_Rumen_uncultured_genome_RUG14912_genomic.fna/dqc_result.json
[2023-06-08 14:29:27,814] [INFO] DFAST_QC completed!
[2023-06-08 14:29:27,814] [INFO] Total running time: 0h1m21s