[2023-06-08 05:13:54,415] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:13:54,423] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:13:54,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference
[2023-06-08 05:13:55,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:13:55,935] [INFO] Task started: Prodigal
[2023-06-08 05:13:55,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg219d62aa-6d5e-4216-8b91-79fce759d886/GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna.gz | prodigal -d GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/cds.fna -a GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:14:12,326] [INFO] Task succeeded: Prodigal
[2023-06-08 05:14:12,327] [INFO] Task started: HMMsearch
[2023-06-08 05:14:12,327] [INFO] Running command: hmmsearch --tblout GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/reference_markers.hmm GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:14:12,580] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:14:12,581] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg219d62aa-6d5e-4216-8b91-79fce759d886/GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna.gz]
[2023-06-08 05:14:12,624] [INFO] Query marker FASTA was written to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/markers.fasta
[2023-06-08 05:14:12,625] [INFO] Task started: Blastn
[2023-06-08 05:14:12,625] [INFO] Running command: blastn -query GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/markers.fasta -db /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/reference_markers.fasta -out GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:13,261] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:13,266] [INFO] Selected 20 target genomes.
[2023-06-08 05:14:13,266] [INFO] Target genome list was writen to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/target_genomes.txt
[2023-06-08 05:14:13,267] [INFO] Task started: fastANI
[2023-06-08 05:14:13,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg219d62aa-6d5e-4216-8b91-79fce759d886/GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna.gz --refList GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/target_genomes.txt --output GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:14:23,082] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:23,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:14:23,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:14:23,094] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:14:23,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:14:23,094] [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=ATCC 19189	GCA_900108375.1	839	839	type	True	78.4612	283	946	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.3804	290	946	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.4722	186	946	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.5086	89	946	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2706	67	946	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2553	81	946	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.0749	55	946	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	75.8957	66	946	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	75.8792	67	946	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	75.7846	67	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:14:23,096] [INFO] DFAST Taxonomy check result was written to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/tc_result.tsv
[2023-06-08 05:14:23,097] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:14:23,098] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:14:23,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/checkm_data
[2023-06-08 05:14:23,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:14:23,136] [INFO] Task started: CheckM
[2023-06-08 05:14:23,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/checkm_input GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/checkm_result
[2023-06-08 05:15:12,678] [INFO] Task succeeded: CheckM
[2023-06-08 05:15:12,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:15:12,701] [INFO] ===== Completeness check finished =====
[2023-06-08 05:15:12,701] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:15:12,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/markers.fasta)
[2023-06-08 05:15:12,702] [INFO] Task started: Blastn
[2023-06-08 05:15:12,702] [INFO] Running command: blastn -query GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/markers.fasta -db /var/lib/cwl/stg274c41a4-b034-436e-b3bc-e3b81dbc5607/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:13,714] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:13,719] [INFO] Selected 20 target genomes.
[2023-06-08 05:15:13,719] [INFO] Target genome list was writen to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:15:13,724] [INFO] Task started: fastANI
[2023-06-08 05:15:13,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg219d62aa-6d5e-4216-8b91-79fce759d886/GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna.gz --refList GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/target_genomes_gtdb.txt --output GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:15:24,783] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:24,810] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:15:24,810] [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_900314995.1	s__Prevotella sp900314995	96.5316	787	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.11	96.50	0.82	0.73	11	conclusive
GCA_900318395.1	s__Prevotella sp900318395	80.6407	457	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	-
GCA_900315035.1	s__Prevotella sp900315035	80.3033	422	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	-
GCA_902784615.1	s__Prevotella sp902784615	79.9843	400	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379425.1	s__Prevotella sp002379425	79.9095	277	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965475.1	s__Prevotella sp017965475	79.84	369	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315695.1	s__Prevotella sp900315695	79.7512	401	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.90	97.22	0.82	0.74	6	-
GCA_900319715.1	s__Prevotella sp900319715	79.7135	388	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	97.29	0.85	0.78	10	-
GCA_902800595.1	s__Prevotella sp902800595	79.7083	349	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.22	0.82	0.82	2	-
GCA_017428805.1	s__Prevotella sp017428805	79.7017	377	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776545.1	s__Prevotella sp902776545	79.6572	423	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.23	97.16	0.83	0.82	3	-
GCA_017547605.1	s__Prevotella sp017547605	79.6204	289	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474845.1	s__Prevotella sp017474845	79.2974	239	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290175.1	s__Prevotella sp016290175	79.0931	307	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965725.1	s__Prevotella sp017965725	78.9427	280	946	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	78.8398	290	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.84	0.73	0.73	2	-
GCA_017650905.1	s__Prevotella sp017650905	78.5959	253	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017518935.1	s__Prevotella sp017518935	78.4911	260	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551005.1	s__Prevotella sp017551005	78.4213	284	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315075.1	s__Prevotella sp900315075	76.7873	87	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-08 05:15:24,812] [INFO] GTDB search result was written to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/result_gtdb.tsv
[2023-06-08 05:15:24,812] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:15:24,816] [INFO] DFAST_QC result json was written to GCA_902786485.1_Rumen_uncultured_genome_RUG13179_genomic.fna/dqc_result.json
[2023-06-08 05:15:24,816] [INFO] DFAST_QC completed!
[2023-06-08 05:15:24,816] [INFO] Total running time: 0h1m30s