[2023-06-08 20:21:34,786] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:21:34,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:21:34,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference
[2023-06-08 20:21:36,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:21:36,267] [INFO] Task started: Prodigal
[2023-06-08 20:21:36,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ef8b7ca-4b7a-4302-a8ea-f95c0140f40b/GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna.gz | prodigal -d GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/cds.fna -a GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:21:55,901] [INFO] Task succeeded: Prodigal
[2023-06-08 20:21:55,902] [INFO] Task started: HMMsearch
[2023-06-08 20:21:55,902] [INFO] Running command: hmmsearch --tblout GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/reference_markers.hmm GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:21:56,150] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:21:56,152] [INFO] Found 6/6 markers.
[2023-06-08 20:21:56,189] [INFO] Query marker FASTA was written to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/markers.fasta
[2023-06-08 20:21:56,189] [INFO] Task started: Blastn
[2023-06-08 20:21:56,189] [INFO] Running command: blastn -query GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/markers.fasta -db /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/reference_markers.fasta -out GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:21:56,801] [INFO] Task succeeded: Blastn
[2023-06-08 20:21:56,805] [INFO] Selected 26 target genomes.
[2023-06-08 20:21:56,805] [INFO] Target genome list was writen to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/target_genomes.txt
[2023-06-08 20:21:56,807] [INFO] Task started: fastANI
[2023-06-08 20:21:56,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef8b7ca-4b7a-4302-a8ea-f95c0140f40b/GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna.gz --refList GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/target_genomes.txt --output GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:22:09,133] [INFO] Task succeeded: fastANI
[2023-06-08 20:22:09,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:22:09,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:22:09,153] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:22:09,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:22:09,153] [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 multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.8248	63	1143	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6291	64	1143	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	76.6049	62	1143	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.5694	65	1143	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.5692	62	1143	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.5317	65	1143	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5203	64	1143	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.4666	92	1143	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.3465	91	1143	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	76.299	52	1143	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.2899	90	1143	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.27	90	1143	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	76.2349	54	1143	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.1865	92	1143	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	76.1563	53	1143	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	76.139	55	1143	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:22:09,156] [INFO] DFAST Taxonomy check result was written to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/tc_result.tsv
[2023-06-08 20:22:09,157] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:22:09,157] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:22:09,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/checkm_data
[2023-06-08 20:22:09,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:22:09,200] [INFO] Task started: CheckM
[2023-06-08 20:22:09,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/checkm_input GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/checkm_result
[2023-06-08 20:23:07,507] [INFO] Task succeeded: CheckM
[2023-06-08 20:23:07,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.89%
Contamintation: 2.60%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-06-08 20:23:07,539] [INFO] ===== Completeness check finished =====
[2023-06-08 20:23:07,540] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:23:07,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/markers.fasta)
[2023-06-08 20:23:07,540] [INFO] Task started: Blastn
[2023-06-08 20:23:07,541] [INFO] Running command: blastn -query GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/markers.fasta -db /var/lib/cwl/stg9357e262-0e26-44db-8d3d-21bb30f6ac4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:23:08,375] [INFO] Task succeeded: Blastn
[2023-06-08 20:23:08,380] [INFO] Selected 18 target genomes.
[2023-06-08 20:23:08,380] [INFO] Target genome list was writen to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:23:08,386] [INFO] Task started: fastANI
[2023-06-08 20:23:08,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef8b7ca-4b7a-4302-a8ea-f95c0140f40b/GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna.gz --refList GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/target_genomes_gtdb.txt --output GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:23:18,884] [INFO] Task succeeded: fastANI
[2023-06-08 20:23:18,902] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:23:18,902] [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_902784755.1	s__Prevotella sp902784755	97.5888	780	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.59	97.59	0.83	0.83	2	conclusive
GCA_900316985.1	s__Prevotella sp900316985	82.7813	587	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.04	0.81	0.71	7	-
GCA_900314655.1	s__Prevotella sp900314655	81.5243	544	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	95.82	0.85	0.71	9	-
GCA_017508965.1	s__Prevotella sp017508965	79.6939	286	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.39	95.39	0.73	0.73	2	-
GCA_017428925.1	s__Prevotella sp017428925	78.8041	342	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350805.1	s__Prevotella sp002350805	78.5356	145	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.30	97.51	0.83	0.79	8	-
GCA_002394385.1	s__Prevotella sp002394385	78.1015	157	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_902782305.1	s__Prevotella sp902782305	77.7706	141	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	96.08	0.74	0.67	4	-
GCA_902799975.1	s__Prevotella sp902799975	77.5681	119	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283605.1	s__Prevotella sp016283605	77.3708	107	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799655.1	s__Prevotella sp902799655	77.3127	121	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557185.1	s__Prevotella sp017557185	77.1057	130	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797505.1	s__Prevotella sp902797505	76.7538	112	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.08	95.72	0.78	0.72	7	-
GCA_016284895.1	s__Prevotella sp016284895	76.7027	103	1143	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	76.6068	87	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
GCA_902801425.1	s__Prevotella sp902801425	76.5653	73	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.51	0.78	0.78	3	-
GCA_017471245.1	s__Prevotella sp017471245	76.5121	139	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
GCA_900544825.1	s__Prevotella sp900544825	76.4177	82	1143	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-08 20:23:18,904] [INFO] GTDB search result was written to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/result_gtdb.tsv
[2023-06-08 20:23:18,905] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:23:18,909] [INFO] DFAST_QC result json was written to GCA_902772175.1_Rumen_uncultured_genome_RUG11740_genomic.fna/dqc_result.json
[2023-06-08 20:23:18,909] [INFO] DFAST_QC completed!
[2023-06-08 20:23:18,909] [INFO] Total running time: 0h1m44s