[2023-03-17 02:45:48,876] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:45:48,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:45:48,876] [INFO] DQC Reference Directory: /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference
[2023-03-17 02:45:50,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:45:50,399] [INFO] Task started: Prodigal
[2023-03-17 02:45:50,399] [INFO] Running command: cat /var/lib/cwl/stgf4ac872a-7856-47e5-9995-8ba559b5908e/OceanDNA-b30044.fa | prodigal -d OceanDNA-b30044/cds.fna -a OceanDNA-b30044/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:45:59,854] [INFO] Task succeeded: Prodigal
[2023-03-17 02:45:59,855] [INFO] Task started: HMMsearch
[2023-03-17 02:45:59,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b30044/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/reference_markers.hmm OceanDNA-b30044/protein.faa > /dev/null
[2023-03-17 02:46:00,004] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:46:00,005] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4ac872a-7856-47e5-9995-8ba559b5908e/OceanDNA-b30044.fa]
[2023-03-17 02:46:00,022] [INFO] Query marker FASTA was written to OceanDNA-b30044/markers.fasta
[2023-03-17 02:46:00,023] [INFO] Task started: Blastn
[2023-03-17 02:46:00,023] [INFO] Running command: blastn -query OceanDNA-b30044/markers.fasta -db /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/reference_markers.fasta -out OceanDNA-b30044/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:46:00,548] [INFO] Task succeeded: Blastn
[2023-03-17 02:46:00,549] [INFO] Selected 19 target genomes.
[2023-03-17 02:46:00,549] [INFO] Target genome list was writen to OceanDNA-b30044/target_genomes.txt
[2023-03-17 02:46:00,632] [INFO] Task started: fastANI
[2023-03-17 02:46:00,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ac872a-7856-47e5-9995-8ba559b5908e/OceanDNA-b30044.fa --refList OceanDNA-b30044/target_genomes.txt --output OceanDNA-b30044/fastani_result.tsv --threads 1
[2023-03-17 02:46:12,532] [INFO] Task succeeded: fastANI
[2023-03-17 02:46:12,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:46:12,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:46:12,535] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:46:12,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:46:12,536] [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
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.9049	52	335	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:46:12,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30044/tc_result.tsv
[2023-03-17 02:46:12,536] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:46:12,536] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:46:12,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/checkm_data
[2023-03-17 02:46:12,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:46:12,550] [INFO] Task started: CheckM
[2023-03-17 02:46:12,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30044/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30044/checkm_input OceanDNA-b30044/checkm_result
[2023-03-17 02:46:40,516] [INFO] Task succeeded: CheckM
[2023-03-17 02:46:40,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:46:40,518] [INFO] ===== Completeness check finished =====
[2023-03-17 02:46:40,518] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:46:40,519] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30044/markers.fasta)
[2023-03-17 02:46:40,519] [INFO] Task started: Blastn
[2023-03-17 02:46:40,520] [INFO] Running command: blastn -query OceanDNA-b30044/markers.fasta -db /var/lib/cwl/stgeda2fcf1-4415-4f25-8a5e-917ea3d5b265/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30044/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:46:41,279] [INFO] Task succeeded: Blastn
[2023-03-17 02:46:41,279] [INFO] Selected 20 target genomes.
[2023-03-17 02:46:41,280] [INFO] Target genome list was writen to OceanDNA-b30044/target_genomes_gtdb.txt
[2023-03-17 02:46:41,567] [INFO] Task started: fastANI
[2023-03-17 02:46:41,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ac872a-7856-47e5-9995-8ba559b5908e/OceanDNA-b30044.fa --refList OceanDNA-b30044/target_genomes_gtdb.txt --output OceanDNA-b30044/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:46:54,008] [INFO] Task succeeded: fastANI
[2023-03-17 02:46:54,011] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:46:54,012] [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
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.477	51	335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.0133	53	335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	75.9049	52	335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:46:54,012] [INFO] GTDB search result was written to OceanDNA-b30044/result_gtdb.tsv
[2023-03-17 02:46:54,012] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:46:54,013] [INFO] DFAST_QC result json was written to OceanDNA-b30044/dqc_result.json
[2023-03-17 02:46:54,014] [INFO] DFAST_QC completed!
[2023-03-17 02:46:54,014] [INFO] Total running time: 0h1m5s