[2023-06-14 00:12:47,651] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:12:47,658] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:12:47,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference
[2023-06-14 00:12:49,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:12:49,412] [INFO] Task started: Prodigal
[2023-06-14 00:12:49,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg443dfe46-2443-4425-a4af-ac6c6ce3c445/GCA_022771065.1_ASM2277106v1_genomic.fna.gz | prodigal -d GCA_022771065.1_ASM2277106v1_genomic.fna/cds.fna -a GCA_022771065.1_ASM2277106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:13:03,922] [INFO] Task succeeded: Prodigal
[2023-06-14 00:13:03,922] [INFO] Task started: HMMsearch
[2023-06-14 00:13:03,922] [INFO] Running command: hmmsearch --tblout GCA_022771065.1_ASM2277106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/reference_markers.hmm GCA_022771065.1_ASM2277106v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:13:04,156] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:13:04,157] [INFO] Found 6/6 markers.
[2023-06-14 00:13:04,198] [INFO] Query marker FASTA was written to GCA_022771065.1_ASM2277106v1_genomic.fna/markers.fasta
[2023-06-14 00:13:04,198] [INFO] Task started: Blastn
[2023-06-14 00:13:04,198] [INFO] Running command: blastn -query GCA_022771065.1_ASM2277106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/reference_markers.fasta -out GCA_022771065.1_ASM2277106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:13:04,782] [INFO] Task succeeded: Blastn
[2023-06-14 00:13:04,785] [INFO] Selected 30 target genomes.
[2023-06-14 00:13:04,786] [INFO] Target genome list was writen to GCA_022771065.1_ASM2277106v1_genomic.fna/target_genomes.txt
[2023-06-14 00:13:04,787] [INFO] Task started: fastANI
[2023-06-14 00:13:04,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg443dfe46-2443-4425-a4af-ac6c6ce3c445/GCA_022771065.1_ASM2277106v1_genomic.fna.gz --refList GCA_022771065.1_ASM2277106v1_genomic.fna/target_genomes.txt --output GCA_022771065.1_ASM2277106v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:13:19,377] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:19,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:13:19,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:13:19,389] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:13:19,389] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 00:13:19,389] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.1831	182	785	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	77.8178	99	785	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.8054	209	785	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.8052	204	785	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.8017	202	785	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	77.7545	101	785	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	77.3732	143	785	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	77.3493	146	785	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.1996	151	785	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.9953	77	785	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	76.8236	91	785	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.7917	124	785	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7524	125	785	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	76.7503	94	785	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.5364	96	785	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.5063	95	785	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.3788	96	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:13:19,394] [INFO] DFAST Taxonomy check result was written to GCA_022771065.1_ASM2277106v1_genomic.fna/tc_result.tsv
[2023-06-14 00:13:19,394] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:13:19,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:13:19,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/checkm_data
[2023-06-14 00:13:19,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:13:19,424] [INFO] Task started: CheckM
[2023-06-14 00:13:19,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022771065.1_ASM2277106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022771065.1_ASM2277106v1_genomic.fna/checkm_input GCA_022771065.1_ASM2277106v1_genomic.fna/checkm_result
[2023-06-14 00:13:59,751] [INFO] Task succeeded: CheckM
[2023-06-14 00:13:59,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-14 00:13:59,783] [INFO] ===== Completeness check finished =====
[2023-06-14 00:13:59,783] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:13:59,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022771065.1_ASM2277106v1_genomic.fna/markers.fasta)
[2023-06-14 00:13:59,784] [INFO] Task started: Blastn
[2023-06-14 00:13:59,784] [INFO] Running command: blastn -query GCA_022771065.1_ASM2277106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef361f37-00e4-428d-a238-03fbc803ff7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022771065.1_ASM2277106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:14:00,773] [INFO] Task succeeded: Blastn
[2023-06-14 00:14:00,777] [INFO] Selected 27 target genomes.
[2023-06-14 00:14:00,777] [INFO] Target genome list was writen to GCA_022771065.1_ASM2277106v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:14:00,779] [INFO] Task started: fastANI
[2023-06-14 00:14:00,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg443dfe46-2443-4425-a4af-ac6c6ce3c445/GCA_022771065.1_ASM2277106v1_genomic.fna.gz --refList GCA_022771065.1_ASM2277106v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022771065.1_ASM2277106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:14:15,883] [INFO] Task succeeded: fastANI
[2023-06-14 00:14:15,896] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:14:15,897] [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_004558865.1	s__Prevotella sp004558865	98.2903	574	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900770845.1	s__Prevotella sp900770845	94.3574	581	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900322035.1	s__Prevotella sp900322035	82.3858	357	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.07	98.30	0.87	0.81	3	-
GCA_900322095.1	s__Prevotella sp900322095	81.2648	392	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.50	99.22	0.86	0.85	3	-
GCA_002437285.1	s__Prevotella sp002437285	78.3529	164	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCF_018789675.1	s__Prevotella sp002300055	78.2028	181	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCF_000518545.1	s__Prevotella seregens	77.8017	202	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
GCA_003447235.1	s__Prevotella sp003447235	77.7588	153	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.02	97.84	0.85	0.82	13	-
GCA_900317685.1	s__Prevotella sp900317685	77.6413	185	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCF_000184945.1	s__Prevotella buccae	77.2182	150	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_905233425.1	s__Prevotella sp905233425	77.2076	137	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546345.1	s__Prevotella sp900546345	77.2051	144	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902779455.1	s__Prevotella sp902779455	77.1521	171	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470345.1	s__Prevotella sp017470345	77.1023	118	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786565.1	s__Prevotella sp902786565	77.0726	151	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.07	98.05	0.87	0.85	3	-
GCA_017474515.1	s__Prevotella sp017474515	76.9726	141	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478085.1	s__Prevotella sp017478085	76.9537	146	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113305.1	s__Prevotella sp900113305	76.9111	138	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774815.1	s__Prevotella sp902774815	76.5232	124	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317545.1	s__Prevotella sp900317545	76.4908	92	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.65	99.65	0.96	0.96	2	-
GCF_000758925.1	s__Prevotella sp000758925	76.3542	67	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:14:15,899] [INFO] GTDB search result was written to GCA_022771065.1_ASM2277106v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:14:15,900] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:14:15,903] [INFO] DFAST_QC result json was written to GCA_022771065.1_ASM2277106v1_genomic.fna/dqc_result.json
[2023-06-14 00:14:15,904] [INFO] DFAST_QC completed!
[2023-06-14 00:14:15,904] [INFO] Total running time: 0h1m28s