[2023-06-17 16:01:46,734] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:01:46,738] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:01:46,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference
[2023-06-17 16:01:48,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:01:48,060] [INFO] Task started: Prodigal
[2023-06-17 16:01:48,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg0364efa0-b491-45a0-8466-ce1cd8f3f217/GCA_009698045.1_ASM969804v1_genomic.fna.gz | prodigal -d GCA_009698045.1_ASM969804v1_genomic.fna/cds.fna -a GCA_009698045.1_ASM969804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:01:50,830] [INFO] Task succeeded: Prodigal
[2023-06-17 16:01:50,831] [INFO] Task started: HMMsearch
[2023-06-17 16:01:50,831] [INFO] Running command: hmmsearch --tblout GCA_009698045.1_ASM969804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/reference_markers.hmm GCA_009698045.1_ASM969804v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:01:51,029] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:01:51,030] [INFO] Found 6/6 markers.
[2023-06-17 16:01:51,048] [INFO] Query marker FASTA was written to GCA_009698045.1_ASM969804v1_genomic.fna/markers.fasta
[2023-06-17 16:01:51,048] [INFO] Task started: Blastn
[2023-06-17 16:01:51,048] [INFO] Running command: blastn -query GCA_009698045.1_ASM969804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/reference_markers.fasta -out GCA_009698045.1_ASM969804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:01:51,709] [INFO] Task succeeded: Blastn
[2023-06-17 16:01:51,714] [INFO] Selected 25 target genomes.
[2023-06-17 16:01:51,715] [INFO] Target genome list was writen to GCA_009698045.1_ASM969804v1_genomic.fna/target_genomes.txt
[2023-06-17 16:01:51,721] [INFO] Task started: fastANI
[2023-06-17 16:01:51,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg0364efa0-b491-45a0-8466-ce1cd8f3f217/GCA_009698045.1_ASM969804v1_genomic.fna.gz --refList GCA_009698045.1_ASM969804v1_genomic.fna/target_genomes.txt --output GCA_009698045.1_ASM969804v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:02:05,425] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:05,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:02:05,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:02:05,429] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:02:05,430] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:02:05,430] [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
--------------------------------------------------------------------------------
[2023-06-17 16:02:05,432] [INFO] DFAST Taxonomy check result was written to GCA_009698045.1_ASM969804v1_genomic.fna/tc_result.tsv
[2023-06-17 16:02:05,433] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:02:05,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:02:05,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/checkm_data
[2023-06-17 16:02:05,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:02:05,455] [INFO] Task started: CheckM
[2023-06-17 16:02:05,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009698045.1_ASM969804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009698045.1_ASM969804v1_genomic.fna/checkm_input GCA_009698045.1_ASM969804v1_genomic.fna/checkm_result
[2023-06-17 16:02:22,613] [INFO] Task succeeded: CheckM
[2023-06-17 16:02:22,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 1.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 16:02:22,643] [INFO] ===== Completeness check finished =====
[2023-06-17 16:02:22,644] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:02:22,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009698045.1_ASM969804v1_genomic.fna/markers.fasta)
[2023-06-17 16:02:22,645] [INFO] Task started: Blastn
[2023-06-17 16:02:22,645] [INFO] Running command: blastn -query GCA_009698045.1_ASM969804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfada86aa-44b3-4d99-a9ee-2ac6ddd93d39/dqc_reference/reference_markers_gtdb.fasta -out GCA_009698045.1_ASM969804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:02:23,656] [INFO] Task succeeded: Blastn
[2023-06-17 16:02:23,661] [INFO] Selected 16 target genomes.
[2023-06-17 16:02:23,661] [INFO] Target genome list was writen to GCA_009698045.1_ASM969804v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:02:23,671] [INFO] Task started: fastANI
[2023-06-17 16:02:23,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg0364efa0-b491-45a0-8466-ce1cd8f3f217/GCA_009698045.1_ASM969804v1_genomic.fna.gz --refList GCA_009698045.1_ASM969804v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009698045.1_ASM969804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:02:27,384] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:27,402] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:02:27,403] [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_009698045.1	s__AAA044-D11 sp009698045	100.0	363	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.24	99.10	0.86	0.82	7	conclusive
GCA_903838035.1	s__AAA044-D11 sp903838035	79.42	108	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.47	98.88	0.87	0.84	8	-
GCA_903898855.1	s__AAA044-D11 sp903898855	78.1441	101	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000485495.1	s__AAA044-D11 sp000485495	78.1408	62	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875815.1	s__AAA044-D11 sp903875815	77.8735	57	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938735.1	s__AAA044-D11 sp903938735	77.549	66	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.02	98.98	0.84	0.83	5	-
GCA_903836945.1	s__AAA044-D11 sp903836945	77.3925	73	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.73	99.63	0.93	0.90	11	-
GCA_903919375.1	s__AAA044-D11 sp903919375	77.3022	76	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.04	98.97	0.88	0.87	4	-
GCA_903842675.1	s__AAA044-D11 sp903842675	76.9193	59	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.43	97.97	0.83	0.78	19	-
GCA_903852585.1	s__PALSA-747 sp903852585	76.9077	57	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.67	99.56	0.92	0.91	12	-
GCA_009701525.1	s__AAA044-D11 sp009701525	76.7218	55	367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:02:27,405] [INFO] GTDB search result was written to GCA_009698045.1_ASM969804v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:02:27,406] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:02:27,410] [INFO] DFAST_QC result json was written to GCA_009698045.1_ASM969804v1_genomic.fna/dqc_result.json
[2023-06-17 16:02:27,410] [INFO] DFAST_QC completed!
[2023-06-17 16:02:27,410] [INFO] Total running time: 0h0m41s