[2023-06-08 19:16:21,046] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:16:21,048] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:16:21,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference
[2023-06-08 19:16:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:16:22,298] [INFO] Task started: Prodigal
[2023-06-08 19:16:22,299] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5c4b389-bd66-4fe0-83f2-e353e905e2b3/GCA_947465415.1_RE-9nov16-381_genomic.fna.gz | prodigal -d GCA_947465415.1_RE-9nov16-381_genomic.fna/cds.fna -a GCA_947465415.1_RE-9nov16-381_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:16:24,147] [INFO] Task succeeded: Prodigal
[2023-06-08 19:16:24,147] [INFO] Task started: HMMsearch
[2023-06-08 19:16:24,147] [INFO] Running command: hmmsearch --tblout GCA_947465415.1_RE-9nov16-381_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/reference_markers.hmm GCA_947465415.1_RE-9nov16-381_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:16:24,305] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:16:24,307] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf5c4b389-bd66-4fe0-83f2-e353e905e2b3/GCA_947465415.1_RE-9nov16-381_genomic.fna.gz]
[2023-06-08 19:16:24,324] [INFO] Query marker FASTA was written to GCA_947465415.1_RE-9nov16-381_genomic.fna/markers.fasta
[2023-06-08 19:16:24,325] [INFO] Task started: Blastn
[2023-06-08 19:16:24,325] [INFO] Running command: blastn -query GCA_947465415.1_RE-9nov16-381_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/reference_markers.fasta -out GCA_947465415.1_RE-9nov16-381_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:16:24,853] [INFO] Task succeeded: Blastn
[2023-06-08 19:16:24,856] [INFO] Selected 10 target genomes.
[2023-06-08 19:16:24,857] [INFO] Target genome list was writen to GCA_947465415.1_RE-9nov16-381_genomic.fna/target_genomes.txt
[2023-06-08 19:16:24,859] [INFO] Task started: fastANI
[2023-06-08 19:16:24,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5c4b389-bd66-4fe0-83f2-e353e905e2b3/GCA_947465415.1_RE-9nov16-381_genomic.fna.gz --refList GCA_947465415.1_RE-9nov16-381_genomic.fna/target_genomes.txt --output GCA_947465415.1_RE-9nov16-381_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:16:29,676] [INFO] Task succeeded: fastANI
[2023-06-08 19:16:29,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:16:29,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:16:29,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:16:29,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:16:29,679] [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
--------------------------------------------------------------------------------
[2023-06-08 19:16:29,681] [INFO] DFAST Taxonomy check result was written to GCA_947465415.1_RE-9nov16-381_genomic.fna/tc_result.tsv
[2023-06-08 19:16:29,682] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:16:29,682] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:16:29,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/checkm_data
[2023-06-08 19:16:29,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:16:29,699] [INFO] Task started: CheckM
[2023-06-08 19:16:29,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947465415.1_RE-9nov16-381_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947465415.1_RE-9nov16-381_genomic.fna/checkm_input GCA_947465415.1_RE-9nov16-381_genomic.fna/checkm_result
[2023-06-08 19:16:43,312] [INFO] Task succeeded: CheckM
[2023-06-08 19:16:43,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:16:43,335] [INFO] ===== Completeness check finished =====
[2023-06-08 19:16:43,336] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:16:43,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947465415.1_RE-9nov16-381_genomic.fna/markers.fasta)
[2023-06-08 19:16:43,337] [INFO] Task started: Blastn
[2023-06-08 19:16:43,337] [INFO] Running command: blastn -query GCA_947465415.1_RE-9nov16-381_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3678ef4-a5e3-4434-be65-fad44b04d2ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_947465415.1_RE-9nov16-381_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:16:44,011] [INFO] Task succeeded: Blastn
[2023-06-08 19:16:44,015] [INFO] Selected 10 target genomes.
[2023-06-08 19:16:44,016] [INFO] Target genome list was writen to GCA_947465415.1_RE-9nov16-381_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:16:44,017] [INFO] Task started: fastANI
[2023-06-08 19:16:44,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5c4b389-bd66-4fe0-83f2-e353e905e2b3/GCA_947465415.1_RE-9nov16-381_genomic.fna.gz --refList GCA_947465415.1_RE-9nov16-381_genomic.fna/target_genomes_gtdb.txt --output GCA_947465415.1_RE-9nov16-381_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:16:46,310] [INFO] Task succeeded: fastANI
[2023-06-08 19:16:46,319] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:16:46,320] [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_009701525.1	s__AAA044-D11 sp009701525	98.8829	191	255	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_009702205.1	s__AAA044-D11 sp009702205	84.4927	176	255	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	80.9574	130	255	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	80.7144	171	255	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	80.1091	140	255	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_007280395.1	s__AAA044-D11 sp007280395	80.1001	116	255	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_002340925.1	s__AAA044-D11 sp002340925	80.0365	129	255	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	79.9461	167	255	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_002367715.1	s__AAA044-D11 sp002367715	78.3908	114	255	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.65	98.65	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-08 19:16:46,322] [INFO] GTDB search result was written to GCA_947465415.1_RE-9nov16-381_genomic.fna/result_gtdb.tsv
[2023-06-08 19:16:46,323] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:16:46,326] [INFO] DFAST_QC result json was written to GCA_947465415.1_RE-9nov16-381_genomic.fna/dqc_result.json
[2023-06-08 19:16:46,326] [INFO] DFAST_QC completed!
[2023-06-08 19:16:46,326] [INFO] Total running time: 0h0m25s