[2023-06-07 22:13:47,079] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:13:47,081] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:13:47,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference
[2023-06-07 22:13:48,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:13:48,531] [INFO] Task started: Prodigal
[2023-06-07 22:13:48,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d3271b4-911e-403c-b46e-14d6378c3d9f/GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna.gz | prodigal -d GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/cds.fna -a GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:14:06,876] [INFO] Task succeeded: Prodigal
[2023-06-07 22:14:06,877] [INFO] Task started: HMMsearch
[2023-06-07 22:14:06,877] [INFO] Running command: hmmsearch --tblout GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/reference_markers.hmm GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:14:07,159] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:14:07,161] [INFO] Found 6/6 markers.
[2023-06-07 22:14:07,196] [INFO] Query marker FASTA was written to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/markers.fasta
[2023-06-07 22:14:07,197] [INFO] Task started: Blastn
[2023-06-07 22:14:07,197] [INFO] Running command: blastn -query GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/reference_markers.fasta -out GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:14:07,804] [INFO] Task succeeded: Blastn
[2023-06-07 22:14:07,808] [INFO] Selected 26 target genomes.
[2023-06-07 22:14:07,808] [INFO] Target genome list was writen to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/target_genomes.txt
[2023-06-07 22:14:07,809] [INFO] Task started: fastANI
[2023-06-07 22:14:07,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d3271b4-911e-403c-b46e-14d6378c3d9f/GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna.gz --refList GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/target_genomes.txt --output GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:14:20,445] [INFO] Task succeeded: fastANI
[2023-06-07 22:14:20,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:14:20,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:14:20,465] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:14:20,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:14:20,465] [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	78.5115	225	1002	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.4559	233	1002	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.3282	185	1002	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.0679	57	1002	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4145	78	1002	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.3926	59	1002	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.3697	92	1002	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.3363	87	1002	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.2953	89	1002	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.2738	85	1002	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.2296	83	1002	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2243	89	1002	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	75.9765	70	1002	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	75.936	72	1002	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	75.9197	55	1002	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	75.8951	56	1002	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	75.8726	54	1002	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:14:20,467] [INFO] DFAST Taxonomy check result was written to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/tc_result.tsv
[2023-06-07 22:14:20,468] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:14:20,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:14:20,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/checkm_data
[2023-06-07 22:14:20,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:14:20,506] [INFO] Task started: CheckM
[2023-06-07 22:14:20,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/checkm_input GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/checkm_result
[2023-06-07 22:15:13,677] [INFO] Task succeeded: CheckM
[2023-06-07 22:15:13,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:15:13,699] [INFO] ===== Completeness check finished =====
[2023-06-07 22:15:13,700] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:15:13,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/markers.fasta)
[2023-06-07 22:15:13,700] [INFO] Task started: Blastn
[2023-06-07 22:15:13,701] [INFO] Running command: blastn -query GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafc21c2-950b-4278-b58b-b3795756a8ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:15:14,530] [INFO] Task succeeded: Blastn
[2023-06-07 22:15:14,534] [INFO] Selected 17 target genomes.
[2023-06-07 22:15:14,535] [INFO] Target genome list was writen to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:15:14,536] [INFO] Task started: fastANI
[2023-06-07 22:15:14,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d3271b4-911e-403c-b46e-14d6378c3d9f/GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna.gz --refList GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/target_genomes_gtdb.txt --output GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:15:24,401] [INFO] Task succeeded: fastANI
[2023-06-07 22:15:24,417] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:15:24,418] [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_902760345.1	s__Prevotella sp902760345	98.6305	766	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.76	97.90	0.82	0.74	7	conclusive
GCA_900314985.1	s__Prevotella sp900314985	80.5694	447	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_902799355.1	s__Prevotella sp902799355	80.2953	413	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.80	96.48	0.80	0.78	3	-
GCA_902800925.1	s__Prevotella sp902800925	80.2266	381	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772585.1	s__Prevotella sp902772585	80.0311	372	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316265.1	s__Prevotella sp900316265	79.943	388	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.64	96.94	0.80	0.66	12	-
GCA_016291085.1	s__Prevotella sp016291085	79.9057	383	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798425.1	s__Prevotella sp902798425	79.8689	377	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.06	97.06	0.85	0.85	2	-
GCA_900313235.1	s__Prevotella sp900313235	79.825	363	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902799655.1	s__Prevotella sp902799655	79.613	360	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799975.1	s__Prevotella sp902799975	79.4212	204	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760315.1	s__Prevotella sp902760315	79.198	332	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286995.1	s__Prevotella sp016286995	79.1575	321	1002	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	78.9593	307	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCA_902788605.1	s__Prevotella sp902788605	78.6378	252	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_017483805.1	s__Prevotella sp017483805	78.2409	256	1002	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	77.2893	85	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-07 22:15:24,420] [INFO] GTDB search result was written to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/result_gtdb.tsv
[2023-06-07 22:15:24,420] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:15:24,425] [INFO] DFAST_QC result json was written to GCA_902793525.1_Rumen_uncultured_genome_RUG13876_genomic.fna/dqc_result.json
[2023-06-07 22:15:24,425] [INFO] DFAST_QC completed!
[2023-06-07 22:15:24,425] [INFO] Total running time: 0h1m37s