[2023-06-29 16:18:16,141] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:18:16,145] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:18:16,145] [INFO] DQC Reference Directory: /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference
[2023-06-29 16:18:17,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:18:17,358] [INFO] Task started: Prodigal
[2023-06-29 16:18:17,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg01fdf0a2-95bd-4b57-8a6e-584abce060da/GCA_023708285.1_ASM2370828v1_genomic.fna.gz | prodigal -d GCA_023708285.1_ASM2370828v1_genomic.fna/cds.fna -a GCA_023708285.1_ASM2370828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:18:32,253] [INFO] Task succeeded: Prodigal
[2023-06-29 16:18:32,254] [INFO] Task started: HMMsearch
[2023-06-29 16:18:32,254] [INFO] Running command: hmmsearch --tblout GCA_023708285.1_ASM2370828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/reference_markers.hmm GCA_023708285.1_ASM2370828v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:18:32,488] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:18:32,490] [INFO] Found 6/6 markers.
[2023-06-29 16:18:32,516] [INFO] Query marker FASTA was written to GCA_023708285.1_ASM2370828v1_genomic.fna/markers.fasta
[2023-06-29 16:18:32,516] [INFO] Task started: Blastn
[2023-06-29 16:18:32,516] [INFO] Running command: blastn -query GCA_023708285.1_ASM2370828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/reference_markers.fasta -out GCA_023708285.1_ASM2370828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:18:33,123] [INFO] Task succeeded: Blastn
[2023-06-29 16:18:33,128] [INFO] Selected 22 target genomes.
[2023-06-29 16:18:33,129] [INFO] Target genome list was writen to GCA_023708285.1_ASM2370828v1_genomic.fna/target_genomes.txt
[2023-06-29 16:18:33,130] [INFO] Task started: fastANI
[2023-06-29 16:18:33,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg01fdf0a2-95bd-4b57-8a6e-584abce060da/GCA_023708285.1_ASM2370828v1_genomic.fna.gz --refList GCA_023708285.1_ASM2370828v1_genomic.fna/target_genomes.txt --output GCA_023708285.1_ASM2370828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:18:46,038] [INFO] Task succeeded: fastANI
[2023-06-29 16:18:46,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:18:46,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:18:46,058] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 16:18:46,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 16:18:46,058] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	97.188	698	834	95	conclusive
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	79.4819	127	834	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	78.5673	133	834	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	78.5089	131	834	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.3762	196	834	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	78.2762	166	834	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.7313	156	834	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.4353	93	834	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.2936	75	834	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	77.1451	62	834	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.1154	104	834	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.0717	86	834	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.0346	89	834	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0245	107	834	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.9954	75	834	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.8944	119	834	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.8093	60	834	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.5403	102	834	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:18:46,060] [INFO] DFAST Taxonomy check result was written to GCA_023708285.1_ASM2370828v1_genomic.fna/tc_result.tsv
[2023-06-29 16:18:46,061] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:18:46,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:18:46,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/checkm_data
[2023-06-29 16:18:46,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:18:46,340] [INFO] Task started: CheckM
[2023-06-29 16:18:46,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708285.1_ASM2370828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708285.1_ASM2370828v1_genomic.fna/checkm_input GCA_023708285.1_ASM2370828v1_genomic.fna/checkm_result
[2023-06-29 16:19:30,801] [INFO] Task succeeded: CheckM
[2023-06-29 16:19:30,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:19:30,823] [INFO] ===== Completeness check finished =====
[2023-06-29 16:19:30,823] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:19:30,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708285.1_ASM2370828v1_genomic.fna/markers.fasta)
[2023-06-29 16:19:30,824] [INFO] Task started: Blastn
[2023-06-29 16:19:30,824] [INFO] Running command: blastn -query GCA_023708285.1_ASM2370828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb892a4fe-896e-4637-92f2-33ad398fd807/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708285.1_ASM2370828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:31,749] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:31,753] [INFO] Selected 11 target genomes.
[2023-06-29 16:19:31,754] [INFO] Target genome list was writen to GCA_023708285.1_ASM2370828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:19:31,755] [INFO] Task started: fastANI
[2023-06-29 16:19:31,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg01fdf0a2-95bd-4b57-8a6e-584abce060da/GCA_023708285.1_ASM2370828v1_genomic.fna.gz --refList GCA_023708285.1_ASM2370828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708285.1_ASM2370828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:19:38,541] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:38,554] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:19:38,554] [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_000235885.1	s__Prevotella stercorea	97.188	698	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	conclusive
GCF_019052365.1	s__Prevotella sp000434975	89.5917	605	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_002265625.1	s__Prevotella sp002265625	80.9564	427	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900550035.1	s__Prevotella sp900550035	80.6863	371	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_002490315.1	s__Prevotella sp002490315	80.4519	323	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544495.1	s__Prevotella sp900544495	80.3303	337	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900552515.1	s__Prevotella sp900552515	80.3097	290	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900553155.1	s__Prevotella sp900553155	79.9862	237	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900546575.1	s__Prevotella sp900546575	79.8446	343	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_017554105.1	s__Prevotella sp017554105	76.8604	105	834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:19:38,556] [INFO] GTDB search result was written to GCA_023708285.1_ASM2370828v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:19:38,557] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:19:38,560] [INFO] DFAST_QC result json was written to GCA_023708285.1_ASM2370828v1_genomic.fna/dqc_result.json
[2023-06-29 16:19:38,561] [INFO] DFAST_QC completed!
[2023-06-29 16:19:38,561] [INFO] Total running time: 0h1m22s