[2024-01-24 14:38:45,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference
[2024-01-24 14:38:48,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,276] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe102b95-a801-4810-a8c3-652f512c394d/GCF_006542645.1_Aond_1.0_genomic.fna.gz | prodigal -d GCF_006542645.1_Aond_1.0_genomic.fna/cds.fna -a GCF_006542645.1_Aond_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:08,846] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:08,846] [INFO] Task started: HMMsearch
[2024-01-24 14:39:08,847] [INFO] Running command: hmmsearch --tblout GCF_006542645.1_Aond_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/reference_markers.hmm GCF_006542645.1_Aond_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:09,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:09,134] [INFO] Found 6/6 markers.
[2024-01-24 14:39:09,163] [INFO] Query marker FASTA was written to GCF_006542645.1_Aond_1.0_genomic.fna/markers.fasta
[2024-01-24 14:39:09,164] [INFO] Task started: Blastn
[2024-01-24 14:39:09,164] [INFO] Running command: blastn -query GCF_006542645.1_Aond_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/reference_markers.fasta -out GCF_006542645.1_Aond_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:09,897] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:09,901] [INFO] Selected 11 target genomes.
[2024-01-24 14:39:09,901] [INFO] Target genome list was writen to GCF_006542645.1_Aond_1.0_genomic.fna/target_genomes.txt
[2024-01-24 14:39:09,906] [INFO] Task started: fastANI
[2024-01-24 14:39:09,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe102b95-a801-4810-a8c3-652f512c394d/GCF_006542645.1_Aond_1.0_genomic.fna.gz --refList GCF_006542645.1_Aond_1.0_genomic.fna/target_genomes.txt --output GCF_006542645.1_Aond_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:18,912] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:18,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:18,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:18,925] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:39:18,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:18,925] [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
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	100.0	1169	1169	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	96.893	978	1169	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	96.8712	979	1169	95	conclusive
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	85.696	736	1169	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	84.2541	656	1169	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	84.0613	660	1169	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.427	602	1169	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	82.3109	582	1169	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	82.3089	578	1169	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	81.8721	586	1169	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.4004	126	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:18,927] [INFO] DFAST Taxonomy check result was written to GCF_006542645.1_Aond_1.0_genomic.fna/tc_result.tsv
[2024-01-24 14:39:18,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:18,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:18,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/checkm_data
[2024-01-24 14:39:18,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:18,967] [INFO] Task started: CheckM
[2024-01-24 14:39:18,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542645.1_Aond_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542645.1_Aond_1.0_genomic.fna/checkm_input GCF_006542645.1_Aond_1.0_genomic.fna/checkm_result
[2024-01-24 14:40:16,802] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:16,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,826] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:16,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:16,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542645.1_Aond_1.0_genomic.fna/markers.fasta)
[2024-01-24 14:40:16,827] [INFO] Task started: Blastn
[2024-01-24 14:40:16,827] [INFO] Running command: blastn -query GCF_006542645.1_Aond_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e24a360-1e24-438c-a912-f8b72fbcb6a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542645.1_Aond_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:17,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:17,903] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:17,903] [INFO] Target genome list was writen to GCF_006542645.1_Aond_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:17,912] [INFO] Task started: fastANI
[2024-01-24 14:40:17,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe102b95-a801-4810-a8c3-652f512c394d/GCF_006542645.1_Aond_1.0_genomic.fna.gz --refList GCF_006542645.1_Aond_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_006542645.1_Aond_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:26,841] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:26,852] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:26,852] [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_000374505.1	s__Alistipes onderdonkii	96.9067	977	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	conclusive
GCF_000265365.1	s__Alistipes finegoldii	85.6962	736	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_902388705.1	s__Alistipes sp902388705	85.4543	718	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCF_000210575.1	s__Alistipes shahii	84.0798	659	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCF_000312145.1	s__Alistipes senegalensis	83.452	587	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_900541585.1	s__Alistipes sp900541585	82.8097	566	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_001941065.1	s__Alistipes sp001941065	82.4476	545	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107675.1	s__Alistipes timonensis	82.3245	581	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCF_900083545.1	s__Alistipes provencensis	82.2916	579	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910576555.1	s__Alistipes sp910576555	81.0882	430	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760675.1	s__Alistipes sp900760675	80.624	508	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290115.1	s__Alistipes excrementigallinarum	80.4535	458	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,854] [INFO] GTDB search result was written to GCF_006542645.1_Aond_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:26,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:26,858] [INFO] DFAST_QC result json was written to GCF_006542645.1_Aond_1.0_genomic.fna/dqc_result.json
[2024-01-24 14:40:26,858] [INFO] DFAST_QC completed!
[2024-01-24 14:40:26,858] [INFO] Total running time: 0h1m41s