[2024-01-25 20:00:50,844] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:50,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:50,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference
[2024-01-25 20:00:52,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:52,010] [INFO] Task started: Prodigal
[2024-01-25 20:00:52,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a5ff2b4-875d-4697-866e-962e45af40d9/GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/cds.fna -a GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:07,568] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:07,568] [INFO] Task started: HMMsearch
[2024-01-25 20:01:07,568] [INFO] Running command: hmmsearch --tblout GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/reference_markers.hmm GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:07,798] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:07,799] [INFO] Found 6/6 markers.
[2024-01-25 20:01:07,828] [INFO] Query marker FASTA was written to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:01:07,828] [INFO] Task started: Blastn
[2024-01-25 20:01:07,828] [INFO] Running command: blastn -query GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/reference_markers.fasta -out GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:08,401] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:08,404] [INFO] Selected 19 target genomes.
[2024-01-25 20:01:08,404] [INFO] Target genome list was writen to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:01:08,421] [INFO] Task started: fastANI
[2024-01-25 20:01:08,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5ff2b4-875d-4697-866e-962e45af40d9/GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna.gz --refList GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:18,508] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:18,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:18,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:18,517] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:01:18,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:18,518] [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	100.0	1177	1178	95	conclusive
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	99.9818	1178	1178	95	conclusive
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	79.3395	250	1178	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.7004	137	1178	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.5913	136	1178	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.5408	140	1178	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.1868	72	1178	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.1865	73	1178	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.0454	97	1178	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9859	89	1178	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.9245	53	1178	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.8363	66	1178	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.8168	72	1178	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.79	55	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:18,519] [INFO] DFAST Taxonomy check result was written to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:01:18,520] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:18,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:18,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/checkm_data
[2024-01-25 20:01:18,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:18,559] [INFO] Task started: CheckM
[2024-01-25 20:01:18,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/checkm_input GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:02:03,982] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:03,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:03,997] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:03,997] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:03,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:02:03,998] [INFO] Task started: Blastn
[2024-01-25 20:02:03,998] [INFO] Running command: blastn -query GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc3bf06-0c22-46f3-8562-b60b7ca4cd7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:04,948] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:04,952] [INFO] Selected 7 target genomes.
[2024-01-25 20:02:04,952] [INFO] Target genome list was writen to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:04,977] [INFO] Task started: fastANI
[2024-01-25 20:02:04,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5ff2b4-875d-4697-866e-962e45af40d9/GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna.gz --refList GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:11,233] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:11,238] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:11,239] [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
GCF_000025925.1	s__Prevotella ruminicola	99.9818	1178	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.74	96.82	0.88	0.80	15	conclusive
GCF_900107775.1	s__Prevotella ruminicola_C	94.3816	937	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.61	0.89	0.89	3	-
GCF_000687715.1	s__Prevotella ruminicola_B	94.2588	916	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789415.1	s__Prevotella sp902789415	90.3587	744	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060625.1	s__Prevotella ruminicola_D	89.3148	855	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619825.1	s__Prevotella sp000619825	85.5687	780	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702825.1	s__Prevotella sp000702825	84.7811	725	1178	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:11,240] [INFO] GTDB search result was written to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:11,240] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:11,243] [INFO] DFAST_QC result json was written to GCF_900108375.1_IMG-taxon_2596583684_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:02:11,243] [INFO] DFAST_QC completed!
[2024-01-25 20:02:11,243] [INFO] Total running time: 0h1m20s