[2023-06-13 11:16:58,995] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:16:58,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:16:58,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference
[2023-06-13 11:17:00,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:17:00,334] [INFO] Task started: Prodigal
[2023-06-13 11:17:00,335] [INFO] Running command: gunzip -c /var/lib/cwl/stga38a85e6-f38b-4a27-b068-a9382e9c09c6/GCA_947482425.1_RH-27jun17-456_genomic.fna.gz | prodigal -d GCA_947482425.1_RH-27jun17-456_genomic.fna/cds.fna -a GCA_947482425.1_RH-27jun17-456_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:17:02,226] [INFO] Task succeeded: Prodigal
[2023-06-13 11:17:02,226] [INFO] Task started: HMMsearch
[2023-06-13 11:17:02,226] [INFO] Running command: hmmsearch --tblout GCA_947482425.1_RH-27jun17-456_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/reference_markers.hmm GCA_947482425.1_RH-27jun17-456_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:17:02,436] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:17:02,438] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga38a85e6-f38b-4a27-b068-a9382e9c09c6/GCA_947482425.1_RH-27jun17-456_genomic.fna.gz]
[2023-06-13 11:17:02,457] [INFO] Query marker FASTA was written to GCA_947482425.1_RH-27jun17-456_genomic.fna/markers.fasta
[2023-06-13 11:17:02,458] [INFO] Task started: Blastn
[2023-06-13 11:17:02,458] [INFO] Running command: blastn -query GCA_947482425.1_RH-27jun17-456_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/reference_markers.fasta -out GCA_947482425.1_RH-27jun17-456_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:17:04,119] [INFO] Task succeeded: Blastn
[2023-06-13 11:17:04,125] [INFO] Selected 19 target genomes.
[2023-06-13 11:17:04,125] [INFO] Target genome list was writen to GCA_947482425.1_RH-27jun17-456_genomic.fna/target_genomes.txt
[2023-06-13 11:17:04,150] [INFO] Task started: fastANI
[2023-06-13 11:17:04,150] [INFO] Running command: fastANI --query /var/lib/cwl/stga38a85e6-f38b-4a27-b068-a9382e9c09c6/GCA_947482425.1_RH-27jun17-456_genomic.fna.gz --refList GCA_947482425.1_RH-27jun17-456_genomic.fna/target_genomes.txt --output GCA_947482425.1_RH-27jun17-456_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:17:08,873] [INFO] Task succeeded: fastANI
[2023-06-13 11:17:08,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:17:08,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:17:08,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:17:08,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:17:08,876] [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
--------------------------------------------------------------------------------
[2023-06-13 11:17:08,880] [INFO] DFAST Taxonomy check result was written to GCA_947482425.1_RH-27jun17-456_genomic.fna/tc_result.tsv
[2023-06-13 11:17:08,881] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:17:08,882] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:17:08,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/checkm_data
[2023-06-13 11:17:08,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:17:08,903] [INFO] Task started: CheckM
[2023-06-13 11:17:08,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947482425.1_RH-27jun17-456_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947482425.1_RH-27jun17-456_genomic.fna/checkm_input GCA_947482425.1_RH-27jun17-456_genomic.fna/checkm_result
[2023-06-13 11:17:23,698] [INFO] Task succeeded: CheckM
[2023-06-13 11:17:23,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:17:23,728] [INFO] ===== Completeness check finished =====
[2023-06-13 11:17:23,728] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:17:23,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947482425.1_RH-27jun17-456_genomic.fna/markers.fasta)
[2023-06-13 11:17:23,729] [INFO] Task started: Blastn
[2023-06-13 11:17:23,729] [INFO] Running command: blastn -query GCA_947482425.1_RH-27jun17-456_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7bfdaf-5504-4e82-ba33-a88e8df0d0fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_947482425.1_RH-27jun17-456_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:17:24,231] [INFO] Task succeeded: Blastn
[2023-06-13 11:17:24,237] [INFO] Selected 7 target genomes.
[2023-06-13 11:17:24,238] [INFO] Target genome list was writen to GCA_947482425.1_RH-27jun17-456_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:17:24,240] [INFO] Task started: fastANI
[2023-06-13 11:17:24,240] [INFO] Running command: fastANI --query /var/lib/cwl/stga38a85e6-f38b-4a27-b068-a9382e9c09c6/GCA_947482425.1_RH-27jun17-456_genomic.fna.gz --refList GCA_947482425.1_RH-27jun17-456_genomic.fna/target_genomes_gtdb.txt --output GCA_947482425.1_RH-27jun17-456_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:17:25,957] [INFO] Task succeeded: fastANI
[2023-06-13 11:17:25,964] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:17:25,965] [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_009702205.1	s__AAA044-D11 sp009702205	99.3052	223	274	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009701525.1	s__AAA044-D11 sp009701525	84.2683	174	274	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_903871555.1	s__AAA044-D11 sp903871555	80.877	175	274	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
GCA_009701575.1	s__AAA044-D11 sp009701575	80.5098	154	274	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	80.2201	139	274	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_009726125.1	s__AAA044-D11 sp009726125	79.8564	172	274	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_007280395.1	s__AAA044-D11 sp007280395	79.8403	137	274	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:17:25,967] [INFO] GTDB search result was written to GCA_947482425.1_RH-27jun17-456_genomic.fna/result_gtdb.tsv
[2023-06-13 11:17:25,967] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:17:25,970] [INFO] DFAST_QC result json was written to GCA_947482425.1_RH-27jun17-456_genomic.fna/dqc_result.json
[2023-06-13 11:17:25,970] [INFO] DFAST_QC completed!
[2023-06-13 11:17:25,970] [INFO] Total running time: 0h0m27s