[2023-06-29 13:36:32,690] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:36:32,692] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:36:32,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference
[2023-06-29 13:36:33,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:36:33,991] [INFO] Task started: Prodigal
[2023-06-29 13:36:33,991] [INFO] Running command: gunzip -c /var/lib/cwl/stgd56b05dd-5504-45ce-8569-b6cd4bf6273c/GCA_910587515.1_MGBC140491_genomic.fna.gz | prodigal -d GCA_910587515.1_MGBC140491_genomic.fna/cds.fna -a GCA_910587515.1_MGBC140491_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:36:46,169] [INFO] Task succeeded: Prodigal
[2023-06-29 13:36:46,170] [INFO] Task started: HMMsearch
[2023-06-29 13:36:46,170] [INFO] Running command: hmmsearch --tblout GCA_910587515.1_MGBC140491_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/reference_markers.hmm GCA_910587515.1_MGBC140491_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:36:46,437] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:36:46,438] [INFO] Found 6/6 markers.
[2023-06-29 13:36:46,469] [INFO] Query marker FASTA was written to GCA_910587515.1_MGBC140491_genomic.fna/markers.fasta
[2023-06-29 13:36:46,469] [INFO] Task started: Blastn
[2023-06-29 13:36:46,469] [INFO] Running command: blastn -query GCA_910587515.1_MGBC140491_genomic.fna/markers.fasta -db /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/reference_markers.fasta -out GCA_910587515.1_MGBC140491_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:36:47,067] [INFO] Task succeeded: Blastn
[2023-06-29 13:36:47,070] [INFO] Selected 25 target genomes.
[2023-06-29 13:36:47,071] [INFO] Target genome list was writen to GCA_910587515.1_MGBC140491_genomic.fna/target_genomes.txt
[2023-06-29 13:36:47,073] [INFO] Task started: fastANI
[2023-06-29 13:36:47,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgd56b05dd-5504-45ce-8569-b6cd4bf6273c/GCA_910587515.1_MGBC140491_genomic.fna.gz --refList GCA_910587515.1_MGBC140491_genomic.fna/target_genomes.txt --output GCA_910587515.1_MGBC140491_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:37:04,170] [INFO] Task succeeded: fastANI
[2023-06-29 13:37:04,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:37:04,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:37:04,182] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:37:04,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:37:04,182] [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 dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.5767	180	777	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.4209	191	777	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	78.0018	65	777	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.8692	110	777	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.4169	58	777	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:37:04,184] [INFO] DFAST Taxonomy check result was written to GCA_910587515.1_MGBC140491_genomic.fna/tc_result.tsv
[2023-06-29 13:37:04,185] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:37:04,185] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:37:04,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/checkm_data
[2023-06-29 13:37:04,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:37:04,217] [INFO] Task started: CheckM
[2023-06-29 13:37:04,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910587515.1_MGBC140491_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910587515.1_MGBC140491_genomic.fna/checkm_input GCA_910587515.1_MGBC140491_genomic.fna/checkm_result
[2023-06-29 13:37:43,748] [INFO] Task succeeded: CheckM
[2023-06-29 13:37:43,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:37:43,770] [INFO] ===== Completeness check finished =====
[2023-06-29 13:37:43,770] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:37:43,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910587515.1_MGBC140491_genomic.fna/markers.fasta)
[2023-06-29 13:37:43,771] [INFO] Task started: Blastn
[2023-06-29 13:37:43,771] [INFO] Running command: blastn -query GCA_910587515.1_MGBC140491_genomic.fna/markers.fasta -db /var/lib/cwl/stg304d2181-a45c-4ac2-82d7-d42063ca53a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_910587515.1_MGBC140491_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:37:44,575] [INFO] Task succeeded: Blastn
[2023-06-29 13:37:44,579] [INFO] Selected 22 target genomes.
[2023-06-29 13:37:44,580] [INFO] Target genome list was writen to GCA_910587515.1_MGBC140491_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:37:44,590] [INFO] Task started: fastANI
[2023-06-29 13:37:44,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgd56b05dd-5504-45ce-8569-b6cd4bf6273c/GCA_910587515.1_MGBC140491_genomic.fna.gz --refList GCA_910587515.1_MGBC140491_genomic.fna/target_genomes_gtdb.txt --output GCA_910587515.1_MGBC140491_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:37:56,256] [INFO] Task succeeded: fastANI
[2023-06-29 13:37:56,273] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:37:56,273] [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_910587515.1	s__Duncaniella sp910587515	100.0	777	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004803915.1	s__Duncaniella dubosii	78.5992	179	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCF_003024805.1	s__Duncaniella muris	78.413	190	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_910577345.1	s__Duncaniella sp910577345	78.2892	175	777	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	78.1089	139	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577335.1	s__Duncaniella sp910577335	78.1004	145	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	95.78	95.78	0.86	0.86	2	-
GCA_910586665.1	s__Duncaniella sp910586665	78.0968	156	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802345.1	s__Duncaniella sp014802345	78.0506	148	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	-
GCA_910578445.1	s__Duncaniella sp910578445	78.0255	193	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544535.1	s__Duncaniella sp900544535	78.0139	168	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803695.1	s__Muribaculum gordoncarteri	77.9656	65	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_910578515.1	s__Duncaniella sp910578515	77.6882	117	777	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	77.6168	134	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.85	97.85	0.77	0.77	2	-
GCA_910587165.1	s__Duncaniella sp910587165	77.2421	74	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494015.1	s__Duncaniella sp002494015	77.0956	59	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.82	98.87	0.95	0.90	8	-
GCA_910586305.1	s__Duncaniella sp910586305	77.0711	73	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588795.1	s__Duncaniella sp910588795	77.0695	73	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	96.60	96.60	0.87	0.87	2	-
GCF_008728965.1	s__Muribaculum faecis	76.3444	58	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.62	99.32	0.94	0.91	9	-
--------------------------------------------------------------------------------
[2023-06-29 13:37:56,276] [INFO] GTDB search result was written to GCA_910587515.1_MGBC140491_genomic.fna/result_gtdb.tsv
[2023-06-29 13:37:56,276] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:37:56,282] [INFO] DFAST_QC result json was written to GCA_910587515.1_MGBC140491_genomic.fna/dqc_result.json
[2023-06-29 13:37:56,282] [INFO] DFAST_QC completed!
[2023-06-29 13:37:56,282] [INFO] Total running time: 0h1m24s