[2023-06-17 17:16:52,896] [INFO] DFAST_QC pipeline started.
[2023-06-17 17:16:52,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 17:16:52,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference
[2023-06-17 17:16:54,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 17:16:54,625] [INFO] Task started: Prodigal
[2023-06-17 17:16:54,625] [INFO] Running command: gunzip -c /var/lib/cwl/stgf919d9ba-d4d4-4c88-8319-ea481ae90fca/GCA_003162255.1_20100900_E1D_genomic.fna.gz | prodigal -d GCA_003162255.1_20100900_E1D_genomic.fna/cds.fna -a GCA_003162255.1_20100900_E1D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 17:17:10,125] [INFO] Task succeeded: Prodigal
[2023-06-17 17:17:10,126] [INFO] Task started: HMMsearch
[2023-06-17 17:17:10,126] [INFO] Running command: hmmsearch --tblout GCA_003162255.1_20100900_E1D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/reference_markers.hmm GCA_003162255.1_20100900_E1D_genomic.fna/protein.faa > /dev/null
[2023-06-17 17:17:10,442] [INFO] Task succeeded: HMMsearch
[2023-06-17 17:17:10,444] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf919d9ba-d4d4-4c88-8319-ea481ae90fca/GCA_003162255.1_20100900_E1D_genomic.fna.gz]
[2023-06-17 17:17:10,490] [INFO] Query marker FASTA was written to GCA_003162255.1_20100900_E1D_genomic.fna/markers.fasta
[2023-06-17 17:17:10,490] [INFO] Task started: Blastn
[2023-06-17 17:17:10,491] [INFO] Running command: blastn -query GCA_003162255.1_20100900_E1D_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/reference_markers.fasta -out GCA_003162255.1_20100900_E1D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:17:11,088] [INFO] Task succeeded: Blastn
[2023-06-17 17:17:11,095] [INFO] Selected 25 target genomes.
[2023-06-17 17:17:11,096] [INFO] Target genome list was writen to GCA_003162255.1_20100900_E1D_genomic.fna/target_genomes.txt
[2023-06-17 17:17:11,124] [INFO] Task started: fastANI
[2023-06-17 17:17:11,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgf919d9ba-d4d4-4c88-8319-ea481ae90fca/GCA_003162255.1_20100900_E1D_genomic.fna.gz --refList GCA_003162255.1_20100900_E1D_genomic.fna/target_genomes.txt --output GCA_003162255.1_20100900_E1D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 17:17:30,625] [INFO] Task succeeded: fastANI
[2023-06-17 17:17:30,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 17:17:30,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 17:17:30,637] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 17:17:30,638] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 17:17:30,638] [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
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.1775	59	1734	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.1774	59	1734	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	75.6922	55	1734	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	75.671	54	1734	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	75.5457	73	1734	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.3188	55	1734	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 17:17:30,640] [INFO] DFAST Taxonomy check result was written to GCA_003162255.1_20100900_E1D_genomic.fna/tc_result.tsv
[2023-06-17 17:17:30,640] [INFO] ===== Taxonomy check completed =====
[2023-06-17 17:17:30,641] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 17:17:30,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/checkm_data
[2023-06-17 17:17:30,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 17:17:30,702] [INFO] Task started: CheckM
[2023-06-17 17:17:30,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003162255.1_20100900_E1D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003162255.1_20100900_E1D_genomic.fna/checkm_input GCA_003162255.1_20100900_E1D_genomic.fna/checkm_result
[2023-06-17 17:18:17,229] [INFO] Task succeeded: CheckM
[2023-06-17 17:18:17,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.90%
Contamintation: 3.12%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 17:18:17,257] [INFO] ===== Completeness check finished =====
[2023-06-17 17:18:17,257] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:18:17,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003162255.1_20100900_E1D_genomic.fna/markers.fasta)
[2023-06-17 17:18:17,258] [INFO] Task started: Blastn
[2023-06-17 17:18:17,258] [INFO] Running command: blastn -query GCA_003162255.1_20100900_E1D_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b9c9d8c-c55d-4b69-807b-3125e8d19bcf/dqc_reference/reference_markers_gtdb.fasta -out GCA_003162255.1_20100900_E1D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:18:18,042] [INFO] Task succeeded: Blastn
[2023-06-17 17:18:18,046] [INFO] Selected 10 target genomes.
[2023-06-17 17:18:18,047] [INFO] Target genome list was writen to GCA_003162255.1_20100900_E1D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:18:18,053] [INFO] Task started: fastANI
[2023-06-17 17:18:18,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgf919d9ba-d4d4-4c88-8319-ea481ae90fca/GCA_003162255.1_20100900_E1D_genomic.fna.gz --refList GCA_003162255.1_20100900_E1D_genomic.fna/target_genomes_gtdb.txt --output GCA_003162255.1_20100900_E1D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:18:29,264] [INFO] Task succeeded: fastANI
[2023-06-17 17:18:29,278] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 17:18:29,279] [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_003162255.1	s__Bog-209 sp003162255	100.0	1708	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.22	99.22	0.83	0.83	2	conclusive
GCA_003131315.1	s__Bog-209 sp003131315	84.5944	926	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
GCA_003139995.1	s__Bog-209 sp003139995	84.068	886	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.91	99.89	0.95	0.94	6	-
GCA_003138955.1	s__Bog-209 sp003138955	82.6811	696	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132325.1	s__Bog-209 sp003132325	82.1239	803	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	98.56	96.57	0.85	0.79	4	-
GCA_003152795.1	s__Bog-209 sp003152795	81.9236	712	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162935.1	s__Bog-209 sp003162935	80.1026	554	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.71	99.50	0.89	0.82	23	-
GCA_003132405.1	s__Bog-209 sp003132405	79.1782	588	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.82	99.57	0.92	0.89	8	-
GCA_017883425.1	s__Sulfotelmatobacter sp017883425	78.3029	247	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289685.1	s__Sulfotelmatobacter sp013289685	76.9998	230	1734	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 17:18:29,281] [INFO] GTDB search result was written to GCA_003162255.1_20100900_E1D_genomic.fna/result_gtdb.tsv
[2023-06-17 17:18:29,281] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:18:29,285] [INFO] DFAST_QC result json was written to GCA_003162255.1_20100900_E1D_genomic.fna/dqc_result.json
[2023-06-17 17:18:29,285] [INFO] DFAST_QC completed!
[2023-06-17 17:18:29,285] [INFO] Total running time: 0h1m36s