[2023-06-08 13:10:31,107] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:10:31,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:10:31,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference
[2023-06-08 13:10:32,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:10:32,380] [INFO] Task started: Prodigal
[2023-06-08 13:10:32,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg5070232a-e199-45ce-9643-10814964f671/GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna.gz | prodigal -d GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/cds.fna -a GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:10:55,029] [INFO] Task succeeded: Prodigal
[2023-06-08 13:10:55,029] [INFO] Task started: HMMsearch
[2023-06-08 13:10:55,030] [INFO] Running command: hmmsearch --tblout GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/reference_markers.hmm GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:10:55,298] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:10:55,299] [INFO] Found 6/6 markers.
[2023-06-08 13:10:55,329] [INFO] Query marker FASTA was written to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/markers.fasta
[2023-06-08 13:10:55,330] [INFO] Task started: Blastn
[2023-06-08 13:10:55,330] [INFO] Running command: blastn -query GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/reference_markers.fasta -out GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:10:55,903] [INFO] Task succeeded: Blastn
[2023-06-08 13:10:55,907] [INFO] Selected 18 target genomes.
[2023-06-08 13:10:55,907] [INFO] Target genome list was writen to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/target_genomes.txt
[2023-06-08 13:10:55,909] [INFO] Task started: fastANI
[2023-06-08 13:10:55,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg5070232a-e199-45ce-9643-10814964f671/GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna.gz --refList GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/target_genomes.txt --output GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:11:04,771] [INFO] Task succeeded: fastANI
[2023-06-08 13:11:04,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:11:04,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:11:04,787] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:11:04,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:11:04,787] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.5917	81	1002	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.3558	56	1002	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.2645	60	1002	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.2607	66	1002	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.073	72	1002	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	75.9464	52	1002	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.8809	59	1002	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:11:04,790] [INFO] DFAST Taxonomy check result was written to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/tc_result.tsv
[2023-06-08 13:11:04,790] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:11:04,791] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:11:04,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/checkm_data
[2023-06-08 13:11:04,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:11:04,833] [INFO] Task started: CheckM
[2023-06-08 13:11:04,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/checkm_input GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/checkm_result
[2023-06-08 13:12:09,080] [INFO] Task succeeded: CheckM
[2023-06-08 13:12:09,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:12:09,107] [INFO] ===== Completeness check finished =====
[2023-06-08 13:12:09,107] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:12:09,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/markers.fasta)
[2023-06-08 13:12:09,107] [INFO] Task started: Blastn
[2023-06-08 13:12:09,108] [INFO] Running command: blastn -query GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af7151d-290b-4909-b950-f0c239696dae/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:12:09,919] [INFO] Task succeeded: Blastn
[2023-06-08 13:12:09,925] [INFO] Selected 18 target genomes.
[2023-06-08 13:12:09,925] [INFO] Target genome list was writen to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:12:09,931] [INFO] Task started: fastANI
[2023-06-08 13:12:09,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg5070232a-e199-45ce-9643-10814964f671/GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna.gz --refList GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/target_genomes_gtdb.txt --output GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:12:21,258] [INFO] Task succeeded: fastANI
[2023-06-08 13:12:21,274] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:12:21,274] [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_900315745.1	s__Prevotella sp900315745	98.4801	903	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	97.86	0.88	0.79	6	conclusive
GCA_902786665.1	s__Prevotella sp902786665	78.3181	359	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.89	0.89	2	-
GCA_902792855.1	s__Prevotella sp902792855	78.299	336	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.67	98.62	0.88	0.82	4	-
GCA_017617615.1	s__Prevotella sp017617615	78.2943	186	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619375.1	s__Prevotella sp017619375	78.2446	331	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524385.1	s__Prevotella sp017524385	78.15	317	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776475.1	s__Prevotella sp902776475	78.1305	299	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.91	0.91	2	-
GCA_016281815.1	s__Prevotella sp016281815	78.0148	279	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767775.1	s__Prevotella sp902767775	77.9721	339	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_017961115.1	s__Prevotella sp017961115	77.9082	259	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795605.1	s__Prevotella sp902795605	77.7669	268	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291595.1	s__Prevotella sp016291595	76.2587	85	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318885.1	s__Prevotella sp900318885	75.6394	69	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_900551055.1	s__Prevotella sp900551055	75.6218	53	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.16	98.15	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-08 13:12:21,283] [INFO] GTDB search result was written to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/result_gtdb.tsv
[2023-06-08 13:12:21,284] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:12:21,288] [INFO] DFAST_QC result json was written to GCA_902800975.1_Rumen_uncultured_genome_RUG14626_genomic.fna/dqc_result.json
[2023-06-08 13:12:21,289] [INFO] DFAST_QC completed!
[2023-06-08 13:12:21,289] [INFO] Total running time: 0h1m50s