[2023-03-18 04:24:34,127] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:24:34,129] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:24:34,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference
[2023-03-18 04:24:35,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:24:35,782] [INFO] Task started: Prodigal
[2023-03-18 04:24:35,782] [INFO] Running command: cat /var/lib/cwl/stgf32c7b78-f2f2-409e-8275-827b0536318f/OceanDNA-b38398.fa | prodigal -d OceanDNA-b38398/cds.fna -a OceanDNA-b38398/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:24:43,414] [INFO] Task succeeded: Prodigal
[2023-03-18 04:24:43,414] [INFO] Task started: HMMsearch
[2023-03-18 04:24:43,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b38398/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/reference_markers.hmm OceanDNA-b38398/protein.faa > /dev/null
[2023-03-18 04:24:43,579] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:24:43,579] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf32c7b78-f2f2-409e-8275-827b0536318f/OceanDNA-b38398.fa]
[2023-03-18 04:24:43,634] [INFO] Query marker FASTA was written to OceanDNA-b38398/markers.fasta
[2023-03-18 04:24:43,634] [INFO] Task started: Blastn
[2023-03-18 04:24:43,634] [INFO] Running command: blastn -query OceanDNA-b38398/markers.fasta -db /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/reference_markers.fasta -out OceanDNA-b38398/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:24:44,256] [INFO] Task succeeded: Blastn
[2023-03-18 04:24:44,341] [INFO] Selected 26 target genomes.
[2023-03-18 04:24:44,342] [INFO] Target genome list was writen to OceanDNA-b38398/target_genomes.txt
[2023-03-18 04:24:44,400] [INFO] Task started: fastANI
[2023-03-18 04:24:44,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32c7b78-f2f2-409e-8275-827b0536318f/OceanDNA-b38398.fa --refList OceanDNA-b38398/target_genomes.txt --output OceanDNA-b38398/fastani_result.tsv --threads 1
[2023-03-18 04:25:00,285] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:00,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:25:00,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:25:00,288] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:25:00,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:25:00,288] [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
Litoricola lipolytica	strain=IMCC 1097	GCA_009650135.1	418701	418701	type	True	77.0078	70	362	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:25:00,290] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38398/tc_result.tsv
[2023-03-18 04:25:00,292] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:25:00,292] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:25:00,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/checkm_data
[2023-03-18 04:25:00,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:25:00,298] [INFO] Task started: CheckM
[2023-03-18 04:25:00,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38398/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38398/checkm_input OceanDNA-b38398/checkm_result
[2023-03-18 04:25:24,514] [INFO] Task succeeded: CheckM
[2023-03-18 04:25:24,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:25:24,655] [INFO] ===== Completeness check finished =====
[2023-03-18 04:25:24,656] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:25:24,656] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38398/markers.fasta)
[2023-03-18 04:25:24,656] [INFO] Task started: Blastn
[2023-03-18 04:25:24,656] [INFO] Running command: blastn -query OceanDNA-b38398/markers.fasta -db /var/lib/cwl/stgae49b4fb-f1e9-469e-96a6-eb2d5d6303e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38398/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:25:25,591] [INFO] Task succeeded: Blastn
[2023-03-18 04:25:25,595] [INFO] Selected 26 target genomes.
[2023-03-18 04:25:25,595] [INFO] Target genome list was writen to OceanDNA-b38398/target_genomes_gtdb.txt
[2023-03-18 04:25:25,697] [INFO] Task started: fastANI
[2023-03-18 04:25:25,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32c7b78-f2f2-409e-8275-827b0536318f/OceanDNA-b38398.fa --refList OceanDNA-b38398/target_genomes_gtdb.txt --output OceanDNA-b38398/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:25:40,565] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:40,568] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:25:40,568] [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_012269655.1	s__Litoricola sp012269655	87.6461	218	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__Litoricola	95.0	98.73	98.73	0.83	0.83	2	-
GCF_009650135.1	s__Litoricola lipolytica	77.0078	70	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__Litoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:25:40,569] [INFO] GTDB search result was written to OceanDNA-b38398/result_gtdb.tsv
[2023-03-18 04:25:40,571] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:25:40,573] [INFO] DFAST_QC result json was written to OceanDNA-b38398/dqc_result.json
[2023-03-18 04:25:40,573] [INFO] DFAST_QC completed!
[2023-03-18 04:25:40,574] [INFO] Total running time: 0h1m6s