[2023-06-13 08:30:26,958] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:30:26,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:30:26,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference
[2023-06-13 08:30:29,073] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:30:29,074] [INFO] Task started: Prodigal
[2023-06-13 08:30:29,074] [INFO] Running command: gunzip -c /var/lib/cwl/stge0184c94-0d5a-43f3-9512-9c60df4617eb/GCA_022764085.1_ASM2276408v1_genomic.fna.gz | prodigal -d GCA_022764085.1_ASM2276408v1_genomic.fna/cds.fna -a GCA_022764085.1_ASM2276408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:30:46,368] [INFO] Task succeeded: Prodigal
[2023-06-13 08:30:46,368] [INFO] Task started: HMMsearch
[2023-06-13 08:30:46,368] [INFO] Running command: hmmsearch --tblout GCA_022764085.1_ASM2276408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/reference_markers.hmm GCA_022764085.1_ASM2276408v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:30:46,634] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:30:46,636] [INFO] Found 6/6 markers.
[2023-06-13 08:30:46,667] [INFO] Query marker FASTA was written to GCA_022764085.1_ASM2276408v1_genomic.fna/markers.fasta
[2023-06-13 08:30:46,668] [INFO] Task started: Blastn
[2023-06-13 08:30:46,668] [INFO] Running command: blastn -query GCA_022764085.1_ASM2276408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/reference_markers.fasta -out GCA_022764085.1_ASM2276408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:30:47,267] [INFO] Task succeeded: Blastn
[2023-06-13 08:30:47,272] [INFO] Selected 26 target genomes.
[2023-06-13 08:30:47,273] [INFO] Target genome list was writen to GCA_022764085.1_ASM2276408v1_genomic.fna/target_genomes.txt
[2023-06-13 08:30:47,278] [INFO] Task started: fastANI
[2023-06-13 08:30:47,278] [INFO] Running command: fastANI --query /var/lib/cwl/stge0184c94-0d5a-43f3-9512-9c60df4617eb/GCA_022764085.1_ASM2276408v1_genomic.fna.gz --refList GCA_022764085.1_ASM2276408v1_genomic.fna/target_genomes.txt --output GCA_022764085.1_ASM2276408v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:30:58,998] [INFO] Task succeeded: fastANI
[2023-06-13 08:30:58,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:30:58,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:30:59,013] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:30:59,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:30:59,013] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.0679	100	898	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.0511	93	898	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.9712	93	898	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.9417	118	898	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.8259	94	898	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.6928	98	898	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6676	107	898	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.6498	100	898	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.5128	78	898	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4874	87	898	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.4665	56	898	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2713	95	898	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.1684	69	898	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.0801	51	898	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	75.9802	79	898	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	75.9655	83	898	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	75.9404	83	898	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:30:59,015] [INFO] DFAST Taxonomy check result was written to GCA_022764085.1_ASM2276408v1_genomic.fna/tc_result.tsv
[2023-06-13 08:30:59,015] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:30:59,016] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:30:59,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/checkm_data
[2023-06-13 08:30:59,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:30:59,068] [INFO] Task started: CheckM
[2023-06-13 08:30:59,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022764085.1_ASM2276408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022764085.1_ASM2276408v1_genomic.fna/checkm_input GCA_022764085.1_ASM2276408v1_genomic.fna/checkm_result
[2023-06-13 08:31:50,305] [INFO] Task succeeded: CheckM
[2023-06-13 08:31:50,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:31:50,328] [INFO] ===== Completeness check finished =====
[2023-06-13 08:31:50,329] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:31:50,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022764085.1_ASM2276408v1_genomic.fna/markers.fasta)
[2023-06-13 08:31:50,330] [INFO] Task started: Blastn
[2023-06-13 08:31:50,330] [INFO] Running command: blastn -query GCA_022764085.1_ASM2276408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a9baa9e-9ada-4e87-959a-3308497a664a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022764085.1_ASM2276408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:31:51,233] [INFO] Task succeeded: Blastn
[2023-06-13 08:31:51,238] [INFO] Selected 25 target genomes.
[2023-06-13 08:31:51,238] [INFO] Target genome list was writen to GCA_022764085.1_ASM2276408v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:31:51,245] [INFO] Task started: fastANI
[2023-06-13 08:31:51,245] [INFO] Running command: fastANI --query /var/lib/cwl/stge0184c94-0d5a-43f3-9512-9c60df4617eb/GCA_022764085.1_ASM2276408v1_genomic.fna.gz --refList GCA_022764085.1_ASM2276408v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022764085.1_ASM2276408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:32:04,187] [INFO] Task succeeded: fastANI
[2023-06-13 08:32:04,214] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:32:04,214] [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_002251435.1	s__Prevotella sp002251435	80.2955	307	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251245.1	s__Prevotella sp002251245	79.7255	328	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.53	98.53	0.91	0.91	2	-
GCA_016302965.1	s__Prevotella sp016302965	78.1275	175	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547005.1	s__Prevotella sp900547005	77.4668	75	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.66	96.14	0.84	0.69	4	-
GCA_002394385.1	s__Prevotella sp002394385	77.1713	133	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_017410365.1	s__Prevotella sp017410365	77.14	122	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
GCA_017474925.1	s__Prevotella sp017474925	77.0731	61	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.19	98.19	0.77	0.77	2	-
GCA_900549175.1	s__Prevotella sp900549175	77.0606	145	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_905216025.1	s__Prevotella sp905216025	77.0428	164	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_905198745.1	s__Prevotella sp905198745	77.0393	98	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458125.1	s__Prevotella sp017458125	77.0093	114	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.42	97.42	0.81	0.81	2	-
GCF_013166545.1	s__Prevotella sp013166545	76.7288	103	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_017623335.1	s__Prevotella sp017623335	76.7206	71	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009494395.1	s__Prevotella sp900546535	76.7051	103	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_900318685.1	s__Prevotella sp900318685	76.6784	96	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	97.52	0.91	0.84	4	-
GCA_017458005.1	s__Prevotella sp017458005	76.6484	93	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_900107705.1	s__Prevotella sp900107705	76.6393	107	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_017554105.1	s__Prevotella sp017554105	76.6223	97	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476785.1	s__Prevotella sp017476785	76.6068	103	898	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	76.5078	130	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_902775975.1	s__Prevotella sp902775975	76.4659	99	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCA_002392835.1	s__Prevotella sp002392835	76.258	87	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.57	97.57	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-13 08:32:04,216] [INFO] GTDB search result was written to GCA_022764085.1_ASM2276408v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:32:04,217] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:32:04,221] [INFO] DFAST_QC result json was written to GCA_022764085.1_ASM2276408v1_genomic.fna/dqc_result.json
[2023-06-13 08:32:04,221] [INFO] DFAST_QC completed!
[2023-06-13 08:32:04,222] [INFO] Total running time: 0h1m37s