[2023-06-13 06:34:01,126] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:34:01,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:34:01,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference
[2023-06-13 06:34:02,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:34:02,464] [INFO] Task started: Prodigal
[2023-06-13 06:34:02,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bb20dd9-380d-4ff0-8371-62ec50584eae/GCA_006227015.1_ASM622701v1_genomic.fna.gz | prodigal -d GCA_006227015.1_ASM622701v1_genomic.fna/cds.fna -a GCA_006227015.1_ASM622701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:34:06,990] [INFO] Task succeeded: Prodigal
[2023-06-13 06:34:06,990] [INFO] Task started: HMMsearch
[2023-06-13 06:34:06,991] [INFO] Running command: hmmsearch --tblout GCA_006227015.1_ASM622701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/reference_markers.hmm GCA_006227015.1_ASM622701v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:34:07,211] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:34:07,212] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4bb20dd9-380d-4ff0-8371-62ec50584eae/GCA_006227015.1_ASM622701v1_genomic.fna.gz]
[2023-06-13 06:34:07,236] [INFO] Query marker FASTA was written to GCA_006227015.1_ASM622701v1_genomic.fna/markers.fasta
[2023-06-13 06:34:07,236] [INFO] Task started: Blastn
[2023-06-13 06:34:07,236] [INFO] Running command: blastn -query GCA_006227015.1_ASM622701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/reference_markers.fasta -out GCA_006227015.1_ASM622701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:07,874] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:07,879] [INFO] Selected 24 target genomes.
[2023-06-13 06:34:07,879] [INFO] Target genome list was writen to GCA_006227015.1_ASM622701v1_genomic.fna/target_genomes.txt
[2023-06-13 06:34:07,885] [INFO] Task started: fastANI
[2023-06-13 06:34:07,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb20dd9-380d-4ff0-8371-62ec50584eae/GCA_006227015.1_ASM622701v1_genomic.fna.gz --refList GCA_006227015.1_ASM622701v1_genomic.fna/target_genomes.txt --output GCA_006227015.1_ASM622701v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:34:22,004] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:22,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:34:22,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:34:22,011] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:34:22,011] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 06:34:22,011] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	76.6068	75	461	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:34:22,013] [INFO] DFAST Taxonomy check result was written to GCA_006227015.1_ASM622701v1_genomic.fna/tc_result.tsv
[2023-06-13 06:34:22,014] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:34:22,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:34:22,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/checkm_data
[2023-06-13 06:34:22,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:34:22,041] [INFO] Task started: CheckM
[2023-06-13 06:34:22,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_006227015.1_ASM622701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_006227015.1_ASM622701v1_genomic.fna/checkm_input GCA_006227015.1_ASM622701v1_genomic.fna/checkm_result
[2023-06-13 06:34:42,610] [INFO] Task succeeded: CheckM
[2023-06-13 06:34:42,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.81%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 06:34:42,633] [INFO] ===== Completeness check finished =====
[2023-06-13 06:34:42,634] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:34:42,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_006227015.1_ASM622701v1_genomic.fna/markers.fasta)
[2023-06-13 06:34:42,634] [INFO] Task started: Blastn
[2023-06-13 06:34:42,634] [INFO] Running command: blastn -query GCA_006227015.1_ASM622701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c71dd9-2f78-42ef-a465-3bb361f61a84/dqc_reference/reference_markers_gtdb.fasta -out GCA_006227015.1_ASM622701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:43,585] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:43,589] [INFO] Selected 19 target genomes.
[2023-06-13 06:34:43,590] [INFO] Target genome list was writen to GCA_006227015.1_ASM622701v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:34:43,598] [INFO] Task started: fastANI
[2023-06-13 06:34:43,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb20dd9-380d-4ff0-8371-62ec50584eae/GCA_006227015.1_ASM622701v1_genomic.fna.gz --refList GCA_006227015.1_ASM622701v1_genomic.fna/target_genomes_gtdb.txt --output GCA_006227015.1_ASM622701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:34:53,241] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:53,250] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:34:53,250] [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_006227015.1	s__Porticoccus sp006227015	99.9999	454	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006226995.1	s__Porticoccus sp006226995	83.123	223	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707685.1	s__Porticoccus sp002707685	76.7387	77	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	76.6068	75	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	-
GCA_002733125.1	s__Porticoccus sp002733125	76.1627	69	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:34:53,252] [INFO] GTDB search result was written to GCA_006227015.1_ASM622701v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:34:53,253] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:34:53,255] [INFO] DFAST_QC result json was written to GCA_006227015.1_ASM622701v1_genomic.fna/dqc_result.json
[2023-06-13 06:34:53,255] [INFO] DFAST_QC completed!
[2023-06-13 06:34:53,255] [INFO] Total running time: 0h0m52s