[2023-06-05 18:03:40,448] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:03:40,463] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:03:40,464] [INFO] DQC Reference Directory: /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference
[2023-06-05 18:03:41,692] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:03:41,693] [INFO] Task started: Prodigal
[2023-06-05 18:03:41,693] [INFO] Running command: gunzip -c /var/lib/cwl/stgf575c73f-a552-4d19-a723-b5bbc8f26ca9/GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna.gz | prodigal -d GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/cds.fna -a GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:04:17,608] [INFO] Task succeeded: Prodigal
[2023-06-05 18:04:17,609] [INFO] Task started: HMMsearch
[2023-06-05 18:04:17,609] [INFO] Running command: hmmsearch --tblout GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/reference_markers.hmm GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:04:18,214] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:04:18,216] [INFO] Found 6/6 markers.
[2023-06-05 18:04:18,278] [INFO] Query marker FASTA was written to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/markers.fasta
[2023-06-05 18:04:18,278] [INFO] Task started: Blastn
[2023-06-05 18:04:18,278] [INFO] Running command: blastn -query GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/markers.fasta -db /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/reference_markers.fasta -out GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:04:19,945] [INFO] Task succeeded: Blastn
[2023-06-05 18:04:19,949] [INFO] Selected 22 target genomes.
[2023-06-05 18:04:19,949] [INFO] Target genome list was writen to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/target_genomes.txt
[2023-06-05 18:04:19,962] [INFO] Task started: fastANI
[2023-06-05 18:04:19,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgf575c73f-a552-4d19-a723-b5bbc8f26ca9/GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna.gz --refList GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/target_genomes.txt --output GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:04:32,645] [INFO] Task succeeded: fastANI
[2023-06-05 18:04:32,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:04:32,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:04:32,669] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:04:32,669] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:04:32,670] [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 ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.7199	309	1047	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.6384	310	1047	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.2467	182	1047	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.256	85	1047	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.1968	53	1047	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.1961	112	1047	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.1869	52	1047	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.1758	112	1047	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	76.1528	52	1047	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.1406	117	1047	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.1061	76	1047	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	75.7035	61	1047	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	75.683	62	1047	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	75.5037	53	1047	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	75.4242	52	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:04:32,672] [INFO] DFAST Taxonomy check result was written to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/tc_result.tsv
[2023-06-05 18:04:32,672] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:04:32,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:04:32,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/checkm_data
[2023-06-05 18:04:32,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:04:32,715] [INFO] Task started: CheckM
[2023-06-05 18:04:32,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/checkm_input GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/checkm_result
[2023-06-05 18:05:53,569] [INFO] Task succeeded: CheckM
[2023-06-05 18:05:53,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 4.92%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-05 18:05:53,593] [INFO] ===== Completeness check finished =====
[2023-06-05 18:05:53,594] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:05:53,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/markers.fasta)
[2023-06-05 18:05:53,595] [INFO] Task started: Blastn
[2023-06-05 18:05:53,595] [INFO] Running command: blastn -query GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/markers.fasta -db /var/lib/cwl/stge0690644-bcfb-42b0-9bd0-a7c581621c5c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:54,444] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:54,448] [INFO] Selected 23 target genomes.
[2023-06-05 18:05:54,448] [INFO] Target genome list was writen to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:05:54,462] [INFO] Task started: fastANI
[2023-06-05 18:05:54,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgf575c73f-a552-4d19-a723-b5bbc8f26ca9/GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna.gz --refList GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/target_genomes_gtdb.txt --output GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:06:10,385] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:10,411] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:06:10,412] [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_900315035.1	s__Prevotella sp900315035	100.0	1041	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	conclusive
GCA_900315525.1	s__Prevotella sp900315525	81.9513	545	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.00	0.84	0.76	10	-
GCA_900319305.1	s__Prevotella sp900319305	80.1757	369	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.65	0.87	0.75	3	-
GCA_900314995.1	s__Prevotella sp900314995	80.1051	448	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.11	96.50	0.82	0.73	11	-
GCA_900318395.1	s__Prevotella sp900318395	79.8809	454	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	-
GCA_902799765.1	s__Prevotella sp902799765	79.8678	408	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.49	95.44	0.80	0.73	3	-
GCF_900110085.1	s__Prevotella sp900110085	79.8467	430	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.82	0.82	3	-
GCA_002342665.1	s__Prevotella sp002342665	79.5663	231	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286575.1	s__Prevotella sp016286575	79.4934	363	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443345.1	s__Prevotella sp017443345	79.4815	378	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784065.1	s__Prevotella sp902784065	79.4247	332	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798285.1	s__Prevotella sp902798285	79.3926	338	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.28	98.28	0.87	0.87	2	-
GCA_902784615.1	s__Prevotella sp902784615	79.2873	344	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771155.1	s__Prevotella sp902771155	79.2493	340	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460765.1	s__Prevotella sp017460765	79.0472	315	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110895.1	s__Prevotella sp900110895	78.8003	293	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.50	96.66	0.93	0.90	3	-
GCA_902784565.1	s__Prevotella sp902784565	78.7589	257	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.90	0.76	0.76	2	-
GCA_002379425.1	s__Prevotella sp002379425	78.6721	224	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234145.1	s__Prevotella sp905234145	78.6479	312	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.84	0.73	0.73	2	-
GCF_000619825.1	s__Prevotella sp000619825	78.6167	303	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800365.1	s__Prevotella sp902800365	78.3338	273	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.33	96.33	0.87	0.87	2	-
GCA_900322175.1	s__Prevotella sp900322175	78.2715	256	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900315075.1	s__Prevotella sp900315075	76.4531	98	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:06:10,414] [INFO] GTDB search result was written to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/result_gtdb.tsv
[2023-06-05 18:06:10,415] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:06:10,434] [INFO] DFAST_QC result json was written to GCA_902758475.1_Rumen_uncultured_genome_RUG10358_genomic.fna/dqc_result.json
[2023-06-05 18:06:10,435] [INFO] DFAST_QC completed!
[2023-06-05 18:06:10,435] [INFO] Total running time: 0h2m30s