[2023-03-19 04:58:34,609] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:58:34,609] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:58:34,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference
[2023-03-19 04:58:36,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:58:36,123] [INFO] Task started: Prodigal
[2023-03-19 04:58:36,123] [INFO] Running command: cat /var/lib/cwl/stg67942a3a-ac2e-45bb-9105-2a010606c13c/OceanDNA-b40020.fa | prodigal -d OceanDNA-b40020/cds.fna -a OceanDNA-b40020/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:58:46,639] [INFO] Task succeeded: Prodigal
[2023-03-19 04:58:46,640] [INFO] Task started: HMMsearch
[2023-03-19 04:58:46,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b40020/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/reference_markers.hmm OceanDNA-b40020/protein.faa > /dev/null
[2023-03-19 04:58:46,810] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:58:46,811] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg67942a3a-ac2e-45bb-9105-2a010606c13c/OceanDNA-b40020.fa]
[2023-03-19 04:58:46,825] [INFO] Query marker FASTA was written to OceanDNA-b40020/markers.fasta
[2023-03-19 04:58:46,826] [INFO] Task started: Blastn
[2023-03-19 04:58:46,826] [INFO] Running command: blastn -query OceanDNA-b40020/markers.fasta -db /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/reference_markers.fasta -out OceanDNA-b40020/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:58:47,460] [INFO] Task succeeded: Blastn
[2023-03-19 04:58:47,461] [INFO] Selected 32 target genomes.
[2023-03-19 04:58:47,462] [INFO] Target genome list was writen to OceanDNA-b40020/target_genomes.txt
[2023-03-19 04:58:47,480] [INFO] Task started: fastANI
[2023-03-19 04:58:47,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg67942a3a-ac2e-45bb-9105-2a010606c13c/OceanDNA-b40020.fa --refList OceanDNA-b40020/target_genomes.txt --output OceanDNA-b40020/fastani_result.tsv --threads 1
[2023-03-19 04:59:06,493] [INFO] Task succeeded: fastANI
[2023-03-19 04:59:06,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:59:06,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:59:06,496] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:59:06,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:59:06,497] [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	77.5206	122	553	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:59:06,497] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40020/tc_result.tsv
[2023-03-19 04:59:06,497] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:59:06,497] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:59:06,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/checkm_data
[2023-03-19 04:59:06,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:59:06,578] [INFO] Task started: CheckM
[2023-03-19 04:59:06,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40020/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40020/checkm_input OceanDNA-b40020/checkm_result
[2023-03-19 04:59:37,394] [INFO] Task succeeded: CheckM
[2023-03-19 04:59:37,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:59:37,397] [INFO] ===== Completeness check finished =====
[2023-03-19 04:59:37,397] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:59:37,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40020/markers.fasta)
[2023-03-19 04:59:37,398] [INFO] Task started: Blastn
[2023-03-19 04:59:37,398] [INFO] Running command: blastn -query OceanDNA-b40020/markers.fasta -db /var/lib/cwl/stg0879bbec-9505-4f3a-9be7-541ce1485301/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40020/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:59:38,538] [INFO] Task succeeded: Blastn
[2023-03-19 04:59:38,539] [INFO] Selected 24 target genomes.
[2023-03-19 04:59:38,539] [INFO] Target genome list was writen to OceanDNA-b40020/target_genomes_gtdb.txt
[2023-03-19 04:59:38,561] [INFO] Task started: fastANI
[2023-03-19 04:59:38,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg67942a3a-ac2e-45bb-9105-2a010606c13c/OceanDNA-b40020.fa --refList OceanDNA-b40020/target_genomes_gtdb.txt --output OceanDNA-b40020/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:59:50,898] [INFO] Task succeeded: fastANI
[2023-03-19 04:59:50,904] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:59:50,904] [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_006226995.1	s__Porticoccus sp006226995	95.3197	282	553	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_006227015.1	s__Porticoccus sp006227015	83.2096	270	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	77.5162	123	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	-
GCA_002707685.1	s__Porticoccus sp002707685	77.4897	129	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002733125.1	s__Porticoccus sp002733125	77.4269	101	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341315.1	s__Porticoccus sp002341315	77.1442	120	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390285.1	s__Porticoccus sp002390285	76.4802	63	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.85	99.48	0.95	0.89	6	-
--------------------------------------------------------------------------------
[2023-03-19 04:59:50,904] [INFO] GTDB search result was written to OceanDNA-b40020/result_gtdb.tsv
[2023-03-19 04:59:50,904] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:59:50,905] [INFO] DFAST_QC result json was written to OceanDNA-b40020/dqc_result.json
[2023-03-19 04:59:50,905] [INFO] DFAST_QC completed!
[2023-03-19 04:59:50,905] [INFO] Total running time: 0h1m16s