[2024-01-24 13:37:27,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference
[2024-01-24 13:37:29,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,056] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,056] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bf00ca9-5c9e-4f6d-a7e8-2acea9da53f4/GCF_031191185.1_ASM3119118v1_genomic.fna.gz | prodigal -d GCF_031191185.1_ASM3119118v1_genomic.fna/cds.fna -a GCF_031191185.1_ASM3119118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:42,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:42,947] [INFO] Task started: HMMsearch
[2024-01-24 13:37:42,948] [INFO] Running command: hmmsearch --tblout GCF_031191185.1_ASM3119118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/reference_markers.hmm GCF_031191185.1_ASM3119118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:43,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:43,181] [INFO] Found 6/6 markers.
[2024-01-24 13:37:43,211] [INFO] Query marker FASTA was written to GCF_031191185.1_ASM3119118v1_genomic.fna/markers.fasta
[2024-01-24 13:37:43,211] [INFO] Task started: Blastn
[2024-01-24 13:37:43,212] [INFO] Running command: blastn -query GCF_031191185.1_ASM3119118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/reference_markers.fasta -out GCF_031191185.1_ASM3119118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:43,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:43,809] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:43,809] [INFO] Target genome list was writen to GCF_031191185.1_ASM3119118v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:43,862] [INFO] Task started: fastANI
[2024-01-24 13:37:43,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bf00ca9-5c9e-4f6d-a7e8-2acea9da53f4/GCF_031191185.1_ASM3119118v1_genomic.fna.gz --refList GCF_031191185.1_ASM3119118v1_genomic.fna/target_genomes.txt --output GCF_031191185.1_ASM3119118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:50,544] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:50,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:50,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:50,555] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:50,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:50,556] [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 nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	99.9947	889	891	95	conclusive
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	99.9923	890	891	95	conclusive
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	99.9103	865	891	95	conclusive
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	86.3363	589	891	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	86.2322	588	891	95	below_threshold
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	84.2567	637	891	95	below_threshold
Prevotella pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	84.1554	636	891	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	84.1186	560	891	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.4892	98	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,557] [INFO] DFAST Taxonomy check result was written to GCF_031191185.1_ASM3119118v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:50,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:50,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:50,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/checkm_data
[2024-01-24 13:37:50,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:50,587] [INFO] Task started: CheckM
[2024-01-24 13:37:50,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031191185.1_ASM3119118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031191185.1_ASM3119118v1_genomic.fna/checkm_input GCF_031191185.1_ASM3119118v1_genomic.fna/checkm_result
[2024-01-24 13:38:32,150] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:32,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:32,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:32,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:32,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031191185.1_ASM3119118v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:32,170] [INFO] Task started: Blastn
[2024-01-24 13:38:32,170] [INFO] Running command: blastn -query GCF_031191185.1_ASM3119118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4584a6af-d061-41f6-94ae-ede7faea2874/dqc_reference/reference_markers_gtdb.fasta -out GCF_031191185.1_ASM3119118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:32,994] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:32,997] [INFO] Selected 9 target genomes.
[2024-01-24 13:38:32,997] [INFO] Target genome list was writen to GCF_031191185.1_ASM3119118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:33,022] [INFO] Task started: fastANI
[2024-01-24 13:38:33,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bf00ca9-5c9e-4f6d-a7e8-2acea9da53f4/GCF_031191185.1_ASM3119118v1_genomic.fna.gz --refList GCF_031191185.1_ASM3119118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031191185.1_ASM3119118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:38,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:38,603] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:38,603] [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_000220235.1	s__Prevotella nigrescens	99.9103	865	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	conclusive
GCF_001953955.1	s__Prevotella intermedia	86.6271	594	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000220255.1	s__Prevotella pallens	84.2526	638	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000613945.1	s__Prevotella falsenii	84.1252	560	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614025.1	s__Prevotella aurantiaca	81.6496	526	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000688375.1	s__Prevotella sp000688375	79.1814	191	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155655.1	s__Prevotella ihumii	79.1116	234	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614065.1	s__Prevotella dentasini	78.7253	126	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:38,605] [INFO] GTDB search result was written to GCF_031191185.1_ASM3119118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:38,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:38,608] [INFO] DFAST_QC result json was written to GCF_031191185.1_ASM3119118v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:38,608] [INFO] DFAST_QC completed!
[2024-01-24 13:38:38,608] [INFO] Total running time: 0h1m11s