[2023-06-05 18:52:28,439] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:52:28,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:52:28,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference
[2023-06-05 18:52:29,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:52:29,657] [INFO] Task started: Prodigal
[2023-06-05 18:52:29,657] [INFO] Running command: gunzip -c /var/lib/cwl/stge0485cec-fc82-4c3e-8eda-72e03e85a592/GCA_934643085.1_ERR7738665_bin.96_genomic.fna.gz | prodigal -d GCA_934643085.1_ERR7738665_bin.96_genomic.fna/cds.fna -a GCA_934643085.1_ERR7738665_bin.96_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:52:37,581] [INFO] Task succeeded: Prodigal
[2023-06-05 18:52:37,581] [INFO] Task started: HMMsearch
[2023-06-05 18:52:37,582] [INFO] Running command: hmmsearch --tblout GCA_934643085.1_ERR7738665_bin.96_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/reference_markers.hmm GCA_934643085.1_ERR7738665_bin.96_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:52:37,853] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:52:37,854] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge0485cec-fc82-4c3e-8eda-72e03e85a592/GCA_934643085.1_ERR7738665_bin.96_genomic.fna.gz]
[2023-06-05 18:52:37,890] [INFO] Query marker FASTA was written to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/markers.fasta
[2023-06-05 18:52:37,890] [INFO] Task started: Blastn
[2023-06-05 18:52:37,890] [INFO] Running command: blastn -query GCA_934643085.1_ERR7738665_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/reference_markers.fasta -out GCA_934643085.1_ERR7738665_bin.96_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:52:38,635] [INFO] Task succeeded: Blastn
[2023-06-05 18:52:38,645] [INFO] Selected 11 target genomes.
[2023-06-05 18:52:38,646] [INFO] Target genome list was writen to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/target_genomes.txt
[2023-06-05 18:52:38,647] [INFO] Task started: fastANI
[2023-06-05 18:52:38,647] [INFO] Running command: fastANI --query /var/lib/cwl/stge0485cec-fc82-4c3e-8eda-72e03e85a592/GCA_934643085.1_ERR7738665_bin.96_genomic.fna.gz --refList GCA_934643085.1_ERR7738665_bin.96_genomic.fna/target_genomes.txt --output GCA_934643085.1_ERR7738665_bin.96_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:52:44,607] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:44,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:52:44,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:52:44,611] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:52:44,611] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:52:44,611] [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
--------------------------------------------------------------------------------
[2023-06-05 18:52:44,613] [INFO] DFAST Taxonomy check result was written to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/tc_result.tsv
[2023-06-05 18:52:44,614] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:52:44,614] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:52:44,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/checkm_data
[2023-06-05 18:52:44,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:52:44,653] [INFO] Task started: CheckM
[2023-06-05 18:52:44,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934643085.1_ERR7738665_bin.96_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934643085.1_ERR7738665_bin.96_genomic.fna/checkm_input GCA_934643085.1_ERR7738665_bin.96_genomic.fna/checkm_result
[2023-06-05 18:53:24,485] [INFO] Task succeeded: CheckM
[2023-06-05 18:53:24,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:53:24,578] [INFO] ===== Completeness check finished =====
[2023-06-05 18:53:24,578] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:53:24,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934643085.1_ERR7738665_bin.96_genomic.fna/markers.fasta)
[2023-06-05 18:53:24,578] [INFO] Task started: Blastn
[2023-06-05 18:53:24,579] [INFO] Running command: blastn -query GCA_934643085.1_ERR7738665_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg806a1a22-32fc-4578-8013-3f893801d9ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_934643085.1_ERR7738665_bin.96_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:53:26,441] [INFO] Task succeeded: Blastn
[2023-06-05 18:53:26,445] [INFO] Selected 13 target genomes.
[2023-06-05 18:53:26,445] [INFO] Target genome list was writen to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:53:26,446] [INFO] Task started: fastANI
[2023-06-05 18:53:26,446] [INFO] Running command: fastANI --query /var/lib/cwl/stge0485cec-fc82-4c3e-8eda-72e03e85a592/GCA_934643085.1_ERR7738665_bin.96_genomic.fna.gz --refList GCA_934643085.1_ERR7738665_bin.96_genomic.fna/target_genomes_gtdb.txt --output GCA_934643085.1_ERR7738665_bin.96_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:53:36,615] [INFO] Task succeeded: fastANI
[2023-06-05 18:53:36,626] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:53:36,626] [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_900553295.1	s__Egerieenecus merdigallinarum	97.6846	528	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Egerieenecus	95.0	98.56	97.85	0.79	0.78	4	conclusive
GCA_900553315.1	s__Egerieenecus sp900553315	79.1846	188	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Egerieenecus	95.0	97.57	97.57	0.79	0.79	2	-
GCA_017936765.1	s__UBA11524 sp017936765	78.4781	192	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
GCA_017938695.1	s__UBA11524 sp017938695	78.3465	194	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056415.1	s__UBA11524 sp015056415	78.113	143	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481825.1	s__UBA11524 sp017481825	78.0233	108	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769075.1	s__UBA11524 sp900769075	78.0092	143	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295665.1	s__HGM11604 sp016295665	77.8934	155	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__HGM11604	95.0	98.69	98.69	0.84	0.84	2	-
GCA_017399225.1	s__UBA11524 sp017399225	77.8324	130	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056325.1	s__UBA11524 sp015056325	77.7708	133	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513475.1	s__UBA11524 sp017513475	77.3704	118	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056155.1	s__UBA11524 sp015056155	77.2197	115	785	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:53:36,629] [INFO] GTDB search result was written to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/result_gtdb.tsv
[2023-06-05 18:53:36,629] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:53:36,632] [INFO] DFAST_QC result json was written to GCA_934643085.1_ERR7738665_bin.96_genomic.fna/dqc_result.json
[2023-06-05 18:53:36,632] [INFO] DFAST_QC completed!
[2023-06-05 18:53:36,633] [INFO] Total running time: 0h1m8s