[2024-01-24 12:47:49,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference
[2024-01-24 12:47:50,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,887] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f31a8dc-d396-4950-8608-08f1a7c81506/GCF_900155655.1_Prevotella_ihuae_genomic.fna.gz | prodigal -d GCF_900155655.1_Prevotella_ihuae_genomic.fna/cds.fna -a GCF_900155655.1_Prevotella_ihuae_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:08,037] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:08,038] [INFO] Task started: HMMsearch
[2024-01-24 12:48:08,038] [INFO] Running command: hmmsearch --tblout GCF_900155655.1_Prevotella_ihuae_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/reference_markers.hmm GCF_900155655.1_Prevotella_ihuae_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:08,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:08,310] [INFO] Found 6/6 markers.
[2024-01-24 12:48:08,339] [INFO] Query marker FASTA was written to GCF_900155655.1_Prevotella_ihuae_genomic.fna/markers.fasta
[2024-01-24 12:48:08,340] [INFO] Task started: Blastn
[2024-01-24 12:48:08,340] [INFO] Running command: blastn -query GCF_900155655.1_Prevotella_ihuae_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/reference_markers.fasta -out GCF_900155655.1_Prevotella_ihuae_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:08,920] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:08,923] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:08,924] [INFO] Target genome list was writen to GCF_900155655.1_Prevotella_ihuae_genomic.fna/target_genomes.txt
[2024-01-24 12:48:08,953] [INFO] Task started: fastANI
[2024-01-24 12:48:08,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f31a8dc-d396-4950-8608-08f1a7c81506/GCF_900155655.1_Prevotella_ihuae_genomic.fna.gz --refList GCF_900155655.1_Prevotella_ihuae_genomic.fna/target_genomes.txt --output GCF_900155655.1_Prevotella_ihuae_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:26,964] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:26,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:26,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:26,989] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:26,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:26,989] [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 ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	100.0	1099	1099	95	conclusive
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	84.6165	374	1099	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	82.8355	292	1099	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	81.122	142	1099	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	80.342	145	1099	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	80.3043	149	1099	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	80.1835	253	1099	95	below_threshold
Prevotella intermedia	strain=NCTC13070	GCA_900455005.1	28131	28131	type	True	80.1155	299	1099	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	80.069	305	1099	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	79.9848	53	1099	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	79.9587	302	1099	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	79.8719	303	1099	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	79.4788	152	1099	95	below_threshold
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	79.1199	228	1099	95	below_threshold
Prevotella nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	79.0533	231	1099	95	below_threshold
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	78.8656	218	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:26,991] [INFO] DFAST Taxonomy check result was written to GCF_900155655.1_Prevotella_ihuae_genomic.fna/tc_result.tsv
[2024-01-24 12:48:26,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:26,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:26,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/checkm_data
[2024-01-24 12:48:26,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:27,029] [INFO] Task started: CheckM
[2024-01-24 12:48:27,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155655.1_Prevotella_ihuae_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155655.1_Prevotella_ihuae_genomic.fna/checkm_input GCF_900155655.1_Prevotella_ihuae_genomic.fna/checkm_result
[2024-01-24 12:49:17,154] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:17,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:17,177] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:17,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:17,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155655.1_Prevotella_ihuae_genomic.fna/markers.fasta)
[2024-01-24 12:49:17,178] [INFO] Task started: Blastn
[2024-01-24 12:49:17,178] [INFO] Running command: blastn -query GCF_900155655.1_Prevotella_ihuae_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9f24232-d11f-4e22-aee4-9622022012fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155655.1_Prevotella_ihuae_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:18,016] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:18,021] [INFO] Selected 20 target genomes.
[2024-01-24 12:49:18,021] [INFO] Target genome list was writen to GCF_900155655.1_Prevotella_ihuae_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:18,046] [INFO] Task started: fastANI
[2024-01-24 12:49:18,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f31a8dc-d396-4950-8608-08f1a7c81506/GCF_900155655.1_Prevotella_ihuae_genomic.fna.gz --refList GCF_900155655.1_Prevotella_ihuae_genomic.fna/target_genomes_gtdb.txt --output GCF_900155655.1_Prevotella_ihuae_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:36,333] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:36,355] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:36,355] [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_900155655.1	s__Prevotella ihumii	100.0	1099	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000262545.1	s__Prevotella bivia	84.7302	201	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	-
GCF_000613345.1	s__Prevotella disiens	83.6123	332	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	97.99	0.90	0.82	7	-
GCF_000613725.1	s__Prevotella pleuritidis	83.2714	62	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.65	0.96	0.96	4	-
GCF_000257925.1	s__Prevotella sp000257925	81.2178	171	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_018127785.1	s__Prevotella scopos	81.147	189	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	81.0323	185	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008016795.1	s__Prevotella brunnea	80.8849	167	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	-
GCF_000220255.1	s__Prevotella pallens	80.5113	246	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_018128065.1	s__Prevotella sp000467895	80.2955	190	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000614025.1	s__Prevotella aurantiaca	80.2285	252	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_001953955.1	s__Prevotella intermedia	80.0772	307	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_900187995.1	s__Prevotella jejuni	79.499	150	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_000613945.1	s__Prevotella falsenii	79.4139	280	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	79.188	141	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220235.1	s__Prevotella nigrescens	78.8824	216	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_018127965.1	s__Prevotella melaninogenica_B	78.8651	150	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_000688375.1	s__Prevotella sp000688375	78.6668	225	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:36,357] [INFO] GTDB search result was written to GCF_900155655.1_Prevotella_ihuae_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:36,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:36,363] [INFO] DFAST_QC result json was written to GCF_900155655.1_Prevotella_ihuae_genomic.fna/dqc_result.json
[2024-01-24 12:49:36,363] [INFO] DFAST_QC completed!
[2024-01-24 12:49:36,363] [INFO] Total running time: 0h1m47s