[2024-01-24 14:55:50,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference
[2024-01-24 14:55:52,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,196] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgb580ab22-ac03-4266-bab2-4322ba782721/GCF_003024805.1_ASM302480v1_genomic.fna.gz | prodigal -d GCF_003024805.1_ASM302480v1_genomic.fna/cds.fna -a GCF_003024805.1_ASM302480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:09,075] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:09,076] [INFO] Task started: HMMsearch
[2024-01-24 14:56:09,076] [INFO] Running command: hmmsearch --tblout GCF_003024805.1_ASM302480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/reference_markers.hmm GCF_003024805.1_ASM302480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:09,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:09,322] [INFO] Found 6/6 markers.
[2024-01-24 14:56:09,350] [INFO] Query marker FASTA was written to GCF_003024805.1_ASM302480v1_genomic.fna/markers.fasta
[2024-01-24 14:56:09,351] [INFO] Task started: Blastn
[2024-01-24 14:56:09,351] [INFO] Running command: blastn -query GCF_003024805.1_ASM302480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/reference_markers.fasta -out GCF_003024805.1_ASM302480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:09,974] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:09,980] [INFO] Selected 17 target genomes.
[2024-01-24 14:56:09,980] [INFO] Target genome list was writen to GCF_003024805.1_ASM302480v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:09,988] [INFO] Task started: fastANI
[2024-01-24 14:56:09,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgb580ab22-ac03-4266-bab2-4322ba782721/GCF_003024805.1_ASM302480v1_genomic.fna.gz --refList GCF_003024805.1_ASM302480v1_genomic.fna/target_genomes.txt --output GCF_003024805.1_ASM302480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:18,600] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:18,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:18,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:18,609] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:18,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:18,609] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	100.0	1037	1046	95	conclusive
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	83.3232	54	1046	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	81.5091	168	1046	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	81.4505	171	1046	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	81.2682	198	1046	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	80.0993	364	1046	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	79.3564	135	1046	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	78.7881	142	1046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:18,611] [INFO] DFAST Taxonomy check result was written to GCF_003024805.1_ASM302480v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:18,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:18,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:18,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/checkm_data
[2024-01-24 14:56:18,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:18,644] [INFO] Task started: CheckM
[2024-01-24 14:56:18,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024805.1_ASM302480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024805.1_ASM302480v1_genomic.fna/checkm_input GCF_003024805.1_ASM302480v1_genomic.fna/checkm_result
[2024-01-24 14:57:10,402] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:10,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:10,421] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:10,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:10,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024805.1_ASM302480v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:10,422] [INFO] Task started: Blastn
[2024-01-24 14:57:10,422] [INFO] Running command: blastn -query GCF_003024805.1_ASM302480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83591641-2e34-4d18-bc47-9024a6554a7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024805.1_ASM302480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:11,386] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:11,389] [INFO] Selected 11 target genomes.
[2024-01-24 14:57:11,389] [INFO] Target genome list was writen to GCF_003024805.1_ASM302480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:11,396] [INFO] Task started: fastANI
[2024-01-24 14:57:11,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgb580ab22-ac03-4266-bab2-4322ba782721/GCF_003024805.1_ASM302480v1_genomic.fna.gz --refList GCF_003024805.1_ASM302480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024805.1_ASM302480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:19,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:19,466] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:19,466] [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_003024805.1	s__Duncaniella muris	100.0	1037	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	conclusive
GCA_900544535.1	s__Duncaniella sp900544535	82.1854	589	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803915.1	s__Duncaniella dubosii	80.1062	364	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCA_910577345.1	s__Duncaniella sp910577345	79.6272	386	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586665.1	s__Duncaniella sp910586665	79.5083	346	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578445.1	s__Duncaniella sp910578445	79.2609	347	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577255.1	s__Duncaniella sp910577255	78.8593	281	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801945.1	s__Duncaniella sp014801945	78.7817	242	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.85	97.85	0.77	0.77	2	-
GCA_910584825.1	s__Duncaniella sp910584825	78.755	249	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587185.1	s__Paramuribaculum sp910587185	78.719	101	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	-
GCA_014802015.1	s__Duncaniella sp014802015	78.356	169	1046	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:19,468] [INFO] GTDB search result was written to GCF_003024805.1_ASM302480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:19,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:19,472] [INFO] DFAST_QC result json was written to GCF_003024805.1_ASM302480v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:19,472] [INFO] DFAST_QC completed!
[2024-01-24 14:57:19,472] [INFO] Total running time: 0h1m29s