[2023-06-27 14:17:24,042] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:17:24,045] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:17:24,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference
[2023-06-27 14:17:25,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:17:25,451] [INFO] Task started: Prodigal
[2023-06-27 14:17:25,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg97e646de-12df-45d4-83a7-3fcac88ac832/GCA_002753135.1_ASM275313v1_genomic.fna.gz | prodigal -d GCA_002753135.1_ASM275313v1_genomic.fna/cds.fna -a GCA_002753135.1_ASM275313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:17:43,738] [INFO] Task succeeded: Prodigal
[2023-06-27 14:17:43,739] [INFO] Task started: HMMsearch
[2023-06-27 14:17:43,739] [INFO] Running command: hmmsearch --tblout GCA_002753135.1_ASM275313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/reference_markers.hmm GCA_002753135.1_ASM275313v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:17:43,990] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:17:43,991] [INFO] Found 6/6 markers.
[2023-06-27 14:17:44,031] [INFO] Query marker FASTA was written to GCA_002753135.1_ASM275313v1_genomic.fna/markers.fasta
[2023-06-27 14:17:44,032] [INFO] Task started: Blastn
[2023-06-27 14:17:44,032] [INFO] Running command: blastn -query GCA_002753135.1_ASM275313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/reference_markers.fasta -out GCA_002753135.1_ASM275313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:17:44,714] [INFO] Task succeeded: Blastn
[2023-06-27 14:17:44,718] [INFO] Selected 30 target genomes.
[2023-06-27 14:17:44,718] [INFO] Target genome list was writen to GCA_002753135.1_ASM275313v1_genomic.fna/target_genomes.txt
[2023-06-27 14:17:44,723] [INFO] Task started: fastANI
[2023-06-27 14:17:44,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e646de-12df-45d4-83a7-3fcac88ac832/GCA_002753135.1_ASM275313v1_genomic.fna.gz --refList GCA_002753135.1_ASM275313v1_genomic.fna/target_genomes.txt --output GCA_002753135.1_ASM275313v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:18:01,425] [INFO] Task succeeded: fastANI
[2023-06-27 14:18:01,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:18:01,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:18:01,428] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:18:01,428] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 14:18:01,428] [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
--------------------------------------------------------------------------------
[2023-06-27 14:18:01,431] [INFO] DFAST Taxonomy check result was written to GCA_002753135.1_ASM275313v1_genomic.fna/tc_result.tsv
[2023-06-27 14:18:01,431] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:18:01,432] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:18:01,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/checkm_data
[2023-06-27 14:18:01,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:18:01,479] [INFO] Task started: CheckM
[2023-06-27 14:18:01,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002753135.1_ASM275313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002753135.1_ASM275313v1_genomic.fna/checkm_input GCA_002753135.1_ASM275313v1_genomic.fna/checkm_result
[2023-06-27 14:18:54,463] [INFO] Task succeeded: CheckM
[2023-06-27 14:18:54,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:18:54,487] [INFO] ===== Completeness check finished =====
[2023-06-27 14:18:54,487] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:18:54,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002753135.1_ASM275313v1_genomic.fna/markers.fasta)
[2023-06-27 14:18:54,488] [INFO] Task started: Blastn
[2023-06-27 14:18:54,488] [INFO] Running command: blastn -query GCA_002753135.1_ASM275313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg363f8d13-778b-4fc0-800a-22396a0ade76/dqc_reference/reference_markers_gtdb.fasta -out GCA_002753135.1_ASM275313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:18:55,618] [INFO] Task succeeded: Blastn
[2023-06-27 14:18:55,624] [INFO] Selected 17 target genomes.
[2023-06-27 14:18:55,624] [INFO] Target genome list was writen to GCA_002753135.1_ASM275313v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:18:55,633] [INFO] Task started: fastANI
[2023-06-27 14:18:55,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e646de-12df-45d4-83a7-3fcac88ac832/GCA_002753135.1_ASM275313v1_genomic.fna.gz --refList GCA_002753135.1_ASM275313v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002753135.1_ASM275313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:19:09,053] [INFO] Task succeeded: fastANI
[2023-06-27 14:19:09,066] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 14:19:09,066] [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_002753135.1	s__Magnetaquicoccus sp002753135	100.0	1238	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__Magnetaquicoccus	95.0	99.97	99.97	0.97	0.97	2	conclusive
GCF_004217665.1	s__Magnetaquicoccus inordinatus	79.8643	525	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__Magnetaquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753095.1	s__Magnetaquicoccus sp002753095	79.1796	545	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__Magnetaquicoccus	95.0	99.94	99.94	0.94	0.93	3	-
GCA_015233035.1	s__HCHbin5 sp015233035	77.372	248	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__HCHbin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015229095.1	s__HCHbin5 sp015229095	77.37	202	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__HCHbin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753505.1	s__HCHbin5 sp002753505	77.3138	260	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__HCHbin5	95.0	98.18	96.53	0.88	0.82	3	-
GCA_015229045.1	s__HA3dbin3 sp015229045	76.6865	78	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__DC0425bin3;g__HA3dbin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011089965.1	s__JAANAU01 sp011089965	76.2325	100	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__JAANAU01	95.0	99.65	99.65	0.89	0.89	2	-
GCA_002753185.1	s__WMHbin3 sp002753185	76.0025	83	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__Magnetaquicoccaceae;g__WMHbin3	95.0	99.94	99.94	0.94	0.94	2	-
GCA_002753665.1	s__DC0425bin3 sp002753665	75.7194	52	1241	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__DC0425bin3;g__DC0425bin3	95.0	99.96	99.96	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-27 14:19:09,068] [INFO] GTDB search result was written to GCA_002753135.1_ASM275313v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:19:09,069] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:19:09,072] [INFO] DFAST_QC result json was written to GCA_002753135.1_ASM275313v1_genomic.fna/dqc_result.json
[2023-06-27 14:19:09,072] [INFO] DFAST_QC completed!
[2023-06-27 14:19:09,072] [INFO] Total running time: 0h1m45s