[2023-06-13 13:52:19,626] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:52:19,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:52:19,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference
[2023-06-13 13:52:22,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:52:22,893] [INFO] Task started: Prodigal
[2023-06-13 13:52:22,894] [INFO] Running command: gunzip -c /var/lib/cwl/stga0fe9bde-ee9c-4466-bd71-13d210a9fc3c/GCA_022732385.1_ASM2273238v1_genomic.fna.gz | prodigal -d GCA_022732385.1_ASM2273238v1_genomic.fna/cds.fna -a GCA_022732385.1_ASM2273238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:52:35,634] [INFO] Task succeeded: Prodigal
[2023-06-13 13:52:35,635] [INFO] Task started: HMMsearch
[2023-06-13 13:52:35,635] [INFO] Running command: hmmsearch --tblout GCA_022732385.1_ASM2273238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/reference_markers.hmm GCA_022732385.1_ASM2273238v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:52:35,861] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:52:35,863] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga0fe9bde-ee9c-4466-bd71-13d210a9fc3c/GCA_022732385.1_ASM2273238v1_genomic.fna.gz]
[2023-06-13 13:52:35,890] [INFO] Query marker FASTA was written to GCA_022732385.1_ASM2273238v1_genomic.fna/markers.fasta
[2023-06-13 13:52:35,891] [INFO] Task started: Blastn
[2023-06-13 13:52:35,891] [INFO] Running command: blastn -query GCA_022732385.1_ASM2273238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/reference_markers.fasta -out GCA_022732385.1_ASM2273238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:52:36,482] [INFO] Task succeeded: Blastn
[2023-06-13 13:52:36,486] [INFO] Selected 17 target genomes.
[2023-06-13 13:52:36,487] [INFO] Target genome list was writen to GCA_022732385.1_ASM2273238v1_genomic.fna/target_genomes.txt
[2023-06-13 13:52:36,490] [INFO] Task started: fastANI
[2023-06-13 13:52:36,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga0fe9bde-ee9c-4466-bd71-13d210a9fc3c/GCA_022732385.1_ASM2273238v1_genomic.fna.gz --refList GCA_022732385.1_ASM2273238v1_genomic.fna/target_genomes.txt --output GCA_022732385.1_ASM2273238v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:52:44,345] [INFO] Task succeeded: fastANI
[2023-06-13 13:52:44,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:52:44,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:52:44,363] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:52:44,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:52:44,363] [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
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.0663	58	451	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.0337	63	451	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	77.0282	58	451	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.0282	58	451	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.0253	59	451	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8696	83	451	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.8354	61	451	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.6472	60	451	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.5911	58	451	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4364	52	451	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:52:44,365] [INFO] DFAST Taxonomy check result was written to GCA_022732385.1_ASM2273238v1_genomic.fna/tc_result.tsv
[2023-06-13 13:52:44,367] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:52:44,367] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:52:44,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/checkm_data
[2023-06-13 13:52:44,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:52:44,396] [INFO] Task started: CheckM
[2023-06-13 13:52:44,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022732385.1_ASM2273238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022732385.1_ASM2273238v1_genomic.fna/checkm_input GCA_022732385.1_ASM2273238v1_genomic.fna/checkm_result
[2023-06-13 13:53:23,562] [INFO] Task succeeded: CheckM
[2023-06-13 13:53:23,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:53:23,592] [INFO] ===== Completeness check finished =====
[2023-06-13 13:53:23,593] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:53:23,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022732385.1_ASM2273238v1_genomic.fna/markers.fasta)
[2023-06-13 13:53:23,593] [INFO] Task started: Blastn
[2023-06-13 13:53:23,594] [INFO] Running command: blastn -query GCA_022732385.1_ASM2273238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502a3232-8481-4baa-9fa2-8f357b678528/dqc_reference/reference_markers_gtdb.fasta -out GCA_022732385.1_ASM2273238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:53:24,406] [INFO] Task succeeded: Blastn
[2023-06-13 13:53:24,410] [INFO] Selected 22 target genomes.
[2023-06-13 13:53:24,410] [INFO] Target genome list was writen to GCA_022732385.1_ASM2273238v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:53:24,416] [INFO] Task started: fastANI
[2023-06-13 13:53:24,416] [INFO] Running command: fastANI --query /var/lib/cwl/stga0fe9bde-ee9c-4466-bd71-13d210a9fc3c/GCA_022732385.1_ASM2273238v1_genomic.fna.gz --refList GCA_022732385.1_ASM2273238v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022732385.1_ASM2273238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:53:35,045] [INFO] Task succeeded: fastANI
[2023-06-13 13:53:35,056] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:53:35,057] [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_003447235.1	s__Prevotella sp003447235	97.5434	327	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.02	97.84	0.85	0.82	13	conclusive
GCA_002479145.1	s__Prevotella sp002479145	79.6167	178	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.80	98.73	0.85	0.84	5	-
GCA_900770845.1	s__Prevotella sp900770845	77.5593	83	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558865.1	s__Prevotella sp004558865	77.4451	83	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	77.1635	64	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCF_000191065.1	s__Prevotella multiformis	77.0337	63	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	-
GCF_900454835.1	s__Prevotella denticola	77.0282	58	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCA_002481295.1	s__Prevotella sp002481295	76.8872	50	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_902790625.1	s__Prevotella sp902790625	76.6659	63	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.16	96.49	0.84	0.82	3	-
GCF_000184945.1	s__Prevotella buccae	76.4364	52	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_017474515.1	s__Prevotella sp017474515	76.3855	53	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:53:35,060] [INFO] GTDB search result was written to GCA_022732385.1_ASM2273238v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:53:35,061] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:53:35,065] [INFO] DFAST_QC result json was written to GCA_022732385.1_ASM2273238v1_genomic.fna/dqc_result.json
[2023-06-13 13:53:35,065] [INFO] DFAST_QC completed!
[2023-06-13 13:53:35,065] [INFO] Total running time: 0h1m15s