[2023-06-13 14:59:17,329] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:59:17,332] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:59:17,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference
[2023-06-13 14:59:18,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:59:18,624] [INFO] Task started: Prodigal
[2023-06-13 14:59:18,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg608c8124-09b0-4def-9faa-7e9e19ef4adf/GCA_022722065.1_ASM2272206v1_genomic.fna.gz | prodigal -d GCA_022722065.1_ASM2272206v1_genomic.fna/cds.fna -a GCA_022722065.1_ASM2272206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:59:30,647] [INFO] Task succeeded: Prodigal
[2023-06-13 14:59:30,648] [INFO] Task started: HMMsearch
[2023-06-13 14:59:30,648] [INFO] Running command: hmmsearch --tblout GCA_022722065.1_ASM2272206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/reference_markers.hmm GCA_022722065.1_ASM2272206v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:59:30,904] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:59:30,905] [INFO] Found 6/6 markers.
[2023-06-13 14:59:30,927] [INFO] Query marker FASTA was written to GCA_022722065.1_ASM2272206v1_genomic.fna/markers.fasta
[2023-06-13 14:59:30,927] [INFO] Task started: Blastn
[2023-06-13 14:59:30,927] [INFO] Running command: blastn -query GCA_022722065.1_ASM2272206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/reference_markers.fasta -out GCA_022722065.1_ASM2272206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:31,524] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:31,527] [INFO] Selected 18 target genomes.
[2023-06-13 14:59:31,528] [INFO] Target genome list was writen to GCA_022722065.1_ASM2272206v1_genomic.fna/target_genomes.txt
[2023-06-13 14:59:31,529] [INFO] Task started: fastANI
[2023-06-13 14:59:31,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg608c8124-09b0-4def-9faa-7e9e19ef4adf/GCA_022722065.1_ASM2272206v1_genomic.fna.gz --refList GCA_022722065.1_ASM2272206v1_genomic.fna/target_genomes.txt --output GCA_022722065.1_ASM2272206v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:41,519] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:41,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:41,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:41,537] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 14:59:41,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:59:41,537] [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 putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	99.618	639	715	95	conclusive
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.2735	297	715	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.1446	300	715	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	80.0641	303	715	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	79.9438	287	715	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	79.8087	301	715	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	79.728	297	715	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	79.6856	302	715	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	79.6514	299	715	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	79.3996	250	715	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	79.2266	278	715	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	79.1178	269	715	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	79.0378	277	715	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	78.9278	261	715	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.5964	93	715	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.222	119	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:59:41,540] [INFO] DFAST Taxonomy check result was written to GCA_022722065.1_ASM2272206v1_genomic.fna/tc_result.tsv
[2023-06-13 14:59:41,540] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:41,540] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:41,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/checkm_data
[2023-06-13 14:59:41,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:41,573] [INFO] Task started: CheckM
[2023-06-13 14:59:41,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022722065.1_ASM2272206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022722065.1_ASM2272206v1_genomic.fna/checkm_input GCA_022722065.1_ASM2272206v1_genomic.fna/checkm_result
[2023-06-13 15:00:18,392] [INFO] Task succeeded: CheckM
[2023-06-13 15:00:18,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:00:18,415] [INFO] ===== Completeness check finished =====
[2023-06-13 15:00:18,415] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:00:18,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022722065.1_ASM2272206v1_genomic.fna/markers.fasta)
[2023-06-13 15:00:18,416] [INFO] Task started: Blastn
[2023-06-13 15:00:18,416] [INFO] Running command: blastn -query GCA_022722065.1_ASM2272206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa34ff29-e49f-48be-9f1a-922940486434/dqc_reference/reference_markers_gtdb.fasta -out GCA_022722065.1_ASM2272206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:00:19,321] [INFO] Task succeeded: Blastn
[2023-06-13 15:00:19,327] [INFO] Selected 24 target genomes.
[2023-06-13 15:00:19,327] [INFO] Target genome list was writen to GCA_022722065.1_ASM2272206v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:00:19,335] [INFO] Task started: fastANI
[2023-06-13 15:00:19,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg608c8124-09b0-4def-9faa-7e9e19ef4adf/GCA_022722065.1_ASM2272206v1_genomic.fna.gz --refList GCA_022722065.1_ASM2272206v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022722065.1_ASM2272206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:00:29,433] [INFO] Task succeeded: fastANI
[2023-06-13 15:00:29,459] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:00:29,459] [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_000154465.1	s__Alistipes putredinis	99.618	639	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	conclusive
GCF_000265365.1	s__Alistipes finegoldii	80.1032	300	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCF_000374505.1	s__Alistipes onderdonkii	79.6532	300	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCA_019118565.1	s__Alistipes avicola	79.5844	301	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.24	99.24	0.96	0.96	2	-
GCF_900107675.1	s__Alistipes timonensis	79.1329	269	715	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	79.0378	277	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900541585.1	s__Alistipes sp900541585	79.014	272	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_900544265.1	s__Alistipes merdavium	79.006	235	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_902388705.1	s__Alistipes sp902388705	78.9257	260	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCA_009774895.1	s__Alistipes sp009774895	78.9109	171	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.77	98.77	0.97	0.97	2	-
GCF_900604385.1	s__Alistipes megaguti	78.9069	235	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.62	97.58	0.76	0.76	3	-
GCA_019119615.1	s__Alistipes stercoravium	78.8831	221	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCA_910577475.1	s__Alistipes sp910577475	78.7958	215	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542505.1	s__Alistipes stercorigallinarum	78.7445	224	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_910575495.1	s__Alistipes sp910575495	78.7296	236	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.23	98.47	0.95	0.90	3	-
GCF_900021155.1	s__Alistipes excrementavium	78.7094	273	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCF_900290115.1	s__Alistipes excrementigallinarum	78.6529	235	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCA_910576555.1	s__Alistipes sp910576555	78.638	245	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014796635.1	s__Alistipes sp014796635	78.5757	107	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553175.1	s__Alistipes sp900553175	78.5436	161	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115745.1	s__Alistipes intestinigallinarum	78.4083	212	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214725.1	s__Alistipes sp905214725	78.1647	191	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574205.1	s__Alistipes sp002362235	77.4871	142	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.85	98.52	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2023-06-13 15:00:29,461] [INFO] GTDB search result was written to GCA_022722065.1_ASM2272206v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:00:29,462] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:00:29,466] [INFO] DFAST_QC result json was written to GCA_022722065.1_ASM2272206v1_genomic.fna/dqc_result.json
[2023-06-13 15:00:29,467] [INFO] DFAST_QC completed!
[2023-06-13 15:00:29,467] [INFO] Total running time: 0h1m12s