[2023-06-08 18:25:09,912] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:25:09,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:25:09,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference
[2023-06-08 18:25:11,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:25:11,280] [INFO] Task started: Prodigal
[2023-06-08 18:25:11,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg56204f05-5d50-4626-b5a6-aff4df131e6b/GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna.gz | prodigal -d GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/cds.fna -a GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:25:28,226] [INFO] Task succeeded: Prodigal
[2023-06-08 18:25:28,227] [INFO] Task started: HMMsearch
[2023-06-08 18:25:28,227] [INFO] Running command: hmmsearch --tblout GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/reference_markers.hmm GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:25:28,494] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:25:28,496] [INFO] Found 6/6 markers.
[2023-06-08 18:25:28,540] [INFO] Query marker FASTA was written to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/markers.fasta
[2023-06-08 18:25:28,541] [INFO] Task started: Blastn
[2023-06-08 18:25:28,541] [INFO] Running command: blastn -query GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/reference_markers.fasta -out GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:29,212] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:29,217] [INFO] Selected 26 target genomes.
[2023-06-08 18:25:29,218] [INFO] Target genome list was writen to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/target_genomes.txt
[2023-06-08 18:25:29,220] [INFO] Task started: fastANI
[2023-06-08 18:25:29,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg56204f05-5d50-4626-b5a6-aff4df131e6b/GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna.gz --refList GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/target_genomes.txt --output GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:25:42,733] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:42,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:25:42,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:25:42,752] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:25:42,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 18:25:42,752] [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	78.3444	183	936	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.223	211	936	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.2065	210	936	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.9217	67	936	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.8923	73	936	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7424	76	936	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.7282	85	936	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4442	99	936	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4019	91	936	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.2752	71	936	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2406	96	936	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.2167	98	936	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.1938	100	936	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.1819	50	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 18:25:42,755] [INFO] DFAST Taxonomy check result was written to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/tc_result.tsv
[2023-06-08 18:25:42,755] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:25:42,756] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:25:42,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/checkm_data
[2023-06-08 18:25:42,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:25:42,788] [INFO] Task started: CheckM
[2023-06-08 18:25:42,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/checkm_input GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/checkm_result
[2023-06-08 18:26:33,220] [INFO] Task succeeded: CheckM
[2023-06-08 18:26:33,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:26:33,239] [INFO] ===== Completeness check finished =====
[2023-06-08 18:26:33,239] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:26:33,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/markers.fasta)
[2023-06-08 18:26:33,240] [INFO] Task started: Blastn
[2023-06-08 18:26:33,240] [INFO] Running command: blastn -query GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a0cb6e2-7e37-436e-8e9c-eadf4ba2c77c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:26:34,170] [INFO] Task succeeded: Blastn
[2023-06-08 18:26:34,175] [INFO] Selected 18 target genomes.
[2023-06-08 18:26:34,175] [INFO] Target genome list was writen to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:26:34,178] [INFO] Task started: fastANI
[2023-06-08 18:26:34,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg56204f05-5d50-4626-b5a6-aff4df131e6b/GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna.gz --refList GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/target_genomes_gtdb.txt --output GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:26:43,923] [INFO] Task succeeded: fastANI
[2023-06-08 18:26:43,949] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:26:43,949] [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_900318795.1	s__Prevotella sp900318795	97.9443	736	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.54	96.27	0.80	0.72	18	conclusive
GCA_002363695.1	s__Prevotella sp002363695	87.5127	365	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342415.1	s__Prevotella sp002342415	80.6608	506	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412705.1	s__Prevotella sp017412705	80.3057	437	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107705.1	s__Prevotella sp900107705	80.1532	387	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_017389705.1	s__Prevotella sp017389705	80.0842	427	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353485.1	s__Prevotella sp002353485	79.896	360	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.45	97.45	0.90	0.90	2	-
GCA_902765585.1	s__Prevotella sp902765585	79.8719	370	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800495.1	s__Prevotella sp902800495	79.7661	261	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017847725.1	s__Prevotella sp017847725	79.5005	285	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017941345.1	s__Prevotella sp017941345	79.389	224	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474925.1	s__Prevotella sp017474925	79.2819	254	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.19	98.19	0.77	0.77	2	-
GCA_016286995.1	s__Prevotella sp016286995	79.1153	340	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800925.1	s__Prevotella sp902800925	79.0127	299	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775975.1	s__Prevotella sp902775975	78.8561	305	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCA_902774925.1	s__Prevotella sp902774925	78.7942	380	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	98.74	0.87	0.87	2	-
GCA_902780025.1	s__Prevotella sp902780025	78.3723	281	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315105.1	s__Prevotella sp900315105	76.2044	98	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-08 18:26:43,951] [INFO] GTDB search result was written to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/result_gtdb.tsv
[2023-06-08 18:26:43,952] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:26:43,956] [INFO] DFAST_QC result json was written to GCA_902765335.1_Rumen_uncultured_genome_RUG11051_genomic.fna/dqc_result.json
[2023-06-08 18:26:43,956] [INFO] DFAST_QC completed!
[2023-06-08 18:26:43,956] [INFO] Total running time: 0h1m34s