[2023-06-17 10:14:06,174] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:14:06,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:14:06,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference
[2023-06-17 10:14:07,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:14:07,627] [INFO] Task started: Prodigal
[2023-06-17 10:14:07,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg2633ad0d-e803-40e1-8509-82c8aedbf311/GCA_028721925.1_ASM2872192v1_genomic.fna.gz | prodigal -d GCA_028721925.1_ASM2872192v1_genomic.fna/cds.fna -a GCA_028721925.1_ASM2872192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:14:23,062] [INFO] Task succeeded: Prodigal
[2023-06-17 10:14:23,062] [INFO] Task started: HMMsearch
[2023-06-17 10:14:23,063] [INFO] Running command: hmmsearch --tblout GCA_028721925.1_ASM2872192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/reference_markers.hmm GCA_028721925.1_ASM2872192v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:14:23,367] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:14:23,368] [INFO] Found 6/6 markers.
[2023-06-17 10:14:23,398] [INFO] Query marker FASTA was written to GCA_028721925.1_ASM2872192v1_genomic.fna/markers.fasta
[2023-06-17 10:14:23,398] [INFO] Task started: Blastn
[2023-06-17 10:14:23,398] [INFO] Running command: blastn -query GCA_028721925.1_ASM2872192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/reference_markers.fasta -out GCA_028721925.1_ASM2872192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:24,020] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:24,025] [INFO] Selected 27 target genomes.
[2023-06-17 10:14:24,025] [INFO] Target genome list was writen to GCA_028721925.1_ASM2872192v1_genomic.fna/target_genomes.txt
[2023-06-17 10:14:24,027] [INFO] Task started: fastANI
[2023-06-17 10:14:24,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg2633ad0d-e803-40e1-8509-82c8aedbf311/GCA_028721925.1_ASM2872192v1_genomic.fna.gz --refList GCA_028721925.1_ASM2872192v1_genomic.fna/target_genomes.txt --output GCA_028721925.1_ASM2872192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:14:39,419] [INFO] Task succeeded: fastANI
[2023-06-17 10:14:39,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:14:39,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:14:39,429] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 10:14:39,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 10:14:39,429] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.3481	59	799	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.1915	123	799	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.8095	61	799	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 10:14:39,432] [INFO] DFAST Taxonomy check result was written to GCA_028721925.1_ASM2872192v1_genomic.fna/tc_result.tsv
[2023-06-17 10:14:39,432] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:14:39,432] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:14:39,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/checkm_data
[2023-06-17 10:14:39,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:14:39,467] [INFO] Task started: CheckM
[2023-06-17 10:14:39,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028721925.1_ASM2872192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028721925.1_ASM2872192v1_genomic.fna/checkm_input GCA_028721925.1_ASM2872192v1_genomic.fna/checkm_result
[2023-06-17 10:15:26,994] [INFO] Task succeeded: CheckM
[2023-06-17 10:15:26,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 10:15:27,034] [INFO] ===== Completeness check finished =====
[2023-06-17 10:15:27,034] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:15:27,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028721925.1_ASM2872192v1_genomic.fna/markers.fasta)
[2023-06-17 10:15:27,035] [INFO] Task started: Blastn
[2023-06-17 10:15:27,035] [INFO] Running command: blastn -query GCA_028721925.1_ASM2872192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3f45d6-75af-41a2-b920-94711a421427/dqc_reference/reference_markers_gtdb.fasta -out GCA_028721925.1_ASM2872192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:15:27,845] [INFO] Task succeeded: Blastn
[2023-06-17 10:15:27,850] [INFO] Selected 17 target genomes.
[2023-06-17 10:15:27,850] [INFO] Target genome list was writen to GCA_028721925.1_ASM2872192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:15:27,862] [INFO] Task started: fastANI
[2023-06-17 10:15:27,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg2633ad0d-e803-40e1-8509-82c8aedbf311/GCA_028721925.1_ASM2872192v1_genomic.fna.gz --refList GCA_028721925.1_ASM2872192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028721925.1_ASM2872192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:15:36,157] [INFO] Task succeeded: fastANI
[2023-06-17 10:15:36,172] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:15:36,172] [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_004556065.1	s__Prevotella sp004556065	97.9609	595	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.47	0.85	0.76	10	conclusive
GCA_004555245.1	s__Prevotella sp004555245	78.7422	204	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.26	98.55	0.94	0.92	3	-
GCA_017462915.1	s__Prevotella sp017462915	77.5562	140	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017424205.1	s__Prevotella sp017424205	77.1963	81	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166595.1	s__Prevotella sp002298815	77.1915	123	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	-
GCA_004792655.1	s__Prevotella sp004792655	76.9258	124	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798615.1	s__Prevotella sp902798615	76.2182	63	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.97	96.95	0.86	0.84	3	-
GCA_905233425.1	s__Prevotella sp905233425	76.0532	64	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285055.1	s__Prevotella sp016285055	75.7934	68	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 10:15:36,174] [INFO] GTDB search result was written to GCA_028721925.1_ASM2872192v1_genomic.fna/result_gtdb.tsv
[2023-06-17 10:15:36,175] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:15:36,178] [INFO] DFAST_QC result json was written to GCA_028721925.1_ASM2872192v1_genomic.fna/dqc_result.json
[2023-06-17 10:15:36,178] [INFO] DFAST_QC completed!
[2023-06-17 10:15:36,178] [INFO] Total running time: 0h1m30s