[2023-06-29 14:32:00,983] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:32:00,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:32:00,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference
[2023-06-29 14:32:02,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:32:02,174] [INFO] Task started: Prodigal
[2023-06-29 14:32:02,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg28950024-cd37-4488-ab23-ba4d544b4070/GCA_023708905.1_ASM2370890v1_genomic.fna.gz | prodigal -d GCA_023708905.1_ASM2370890v1_genomic.fna/cds.fna -a GCA_023708905.1_ASM2370890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:32:20,069] [INFO] Task succeeded: Prodigal
[2023-06-29 14:32:20,070] [INFO] Task started: HMMsearch
[2023-06-29 14:32:20,070] [INFO] Running command: hmmsearch --tblout GCA_023708905.1_ASM2370890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/reference_markers.hmm GCA_023708905.1_ASM2370890v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:32:20,342] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:32:20,344] [INFO] Found 6/6 markers.
[2023-06-29 14:32:20,377] [INFO] Query marker FASTA was written to GCA_023708905.1_ASM2370890v1_genomic.fna/markers.fasta
[2023-06-29 14:32:20,377] [INFO] Task started: Blastn
[2023-06-29 14:32:20,377] [INFO] Running command: blastn -query GCA_023708905.1_ASM2370890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/reference_markers.fasta -out GCA_023708905.1_ASM2370890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:32:21,062] [INFO] Task succeeded: Blastn
[2023-06-29 14:32:21,066] [INFO] Selected 11 target genomes.
[2023-06-29 14:32:21,066] [INFO] Target genome list was writen to GCA_023708905.1_ASM2370890v1_genomic.fna/target_genomes.txt
[2023-06-29 14:32:21,067] [INFO] Task started: fastANI
[2023-06-29 14:32:21,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg28950024-cd37-4488-ab23-ba4d544b4070/GCA_023708905.1_ASM2370890v1_genomic.fna.gz --refList GCA_023708905.1_ASM2370890v1_genomic.fna/target_genomes.txt --output GCA_023708905.1_ASM2370890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:32:29,422] [INFO] Task succeeded: fastANI
[2023-06-29 14:32:29,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:32:29,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:32:29,432] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2023-06-29 14:32:29,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 14:32:29,433] [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	98.1871	945	1017	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	97.6185	923	1017	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	97.5216	929	1017	95	conclusive
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	84.8989	670	1017	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	83.266	599	1017	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	83.2452	605	1017	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.2091	561	1017	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	82.3137	542	1017	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	82.2803	559	1017	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	81.809	568	1017	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.707	122	1017	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:32:29,436] [INFO] DFAST Taxonomy check result was written to GCA_023708905.1_ASM2370890v1_genomic.fna/tc_result.tsv
[2023-06-29 14:32:29,436] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:32:29,437] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:32:29,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/checkm_data
[2023-06-29 14:32:29,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:32:29,474] [INFO] Task started: CheckM
[2023-06-29 14:32:29,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708905.1_ASM2370890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708905.1_ASM2370890v1_genomic.fna/checkm_input GCA_023708905.1_ASM2370890v1_genomic.fna/checkm_result
[2023-06-29 14:33:18,430] [INFO] Task succeeded: CheckM
[2023-06-29 14:33:18,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:33:18,454] [INFO] ===== Completeness check finished =====
[2023-06-29 14:33:18,455] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:33:18,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708905.1_ASM2370890v1_genomic.fna/markers.fasta)
[2023-06-29 14:33:18,455] [INFO] Task started: Blastn
[2023-06-29 14:33:18,456] [INFO] Running command: blastn -query GCA_023708905.1_ASM2370890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66df459-50e1-4eb1-9542-1b3c72a2410f/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708905.1_ASM2370890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:33:19,439] [INFO] Task succeeded: Blastn
[2023-06-29 14:33:19,443] [INFO] Selected 12 target genomes.
[2023-06-29 14:33:19,444] [INFO] Target genome list was writen to GCA_023708905.1_ASM2370890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:33:19,445] [INFO] Task started: fastANI
[2023-06-29 14:33:19,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg28950024-cd37-4488-ab23-ba4d544b4070/GCA_023708905.1_ASM2370890v1_genomic.fna.gz --refList GCA_023708905.1_ASM2370890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708905.1_ASM2370890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:33:27,584] [INFO] Task succeeded: fastANI
[2023-06-29 14:33:27,600] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:33:27,600] [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	97.537	929	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	conclusive
GCA_902388705.1	s__Alistipes sp902388705	85.5881	701	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCF_000265365.1	s__Alistipes finegoldii	84.8985	670	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCF_000210575.1	s__Alistipes shahii	83.2558	604	1017	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	83.192	565	1017	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	82.7737	544	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_900107675.1	s__Alistipes timonensis	82.3137	542	1017	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	82.2803	559	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001941065.1	s__Alistipes sp001941065	82.1533	533	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115605.1	s__Alistipes faecigallinarum	81.0587	439	1017	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	80.3362	441	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
--------------------------------------------------------------------------------
[2023-06-29 14:33:27,602] [INFO] GTDB search result was written to GCA_023708905.1_ASM2370890v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:33:27,603] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:33:27,607] [INFO] DFAST_QC result json was written to GCA_023708905.1_ASM2370890v1_genomic.fna/dqc_result.json
[2023-06-29 14:33:27,607] [INFO] DFAST_QC completed!
[2023-06-29 14:33:27,607] [INFO] Total running time: 0h1m27s