[2023-03-18 20:13:32,250] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,251] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference
[2023-03-18 20:13:33,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stg2bc5ad87-b54e-4107-904a-352ab7d9237b/OceanDNA-a4396.fa | prodigal -d OceanDNA-a4396/cds.fna -a OceanDNA-a4396/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:43,240] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:43,240] [INFO] Task started: HMMsearch
[2023-03-18 20:13:43,240] [INFO] Running command: hmmsearch --tblout OceanDNA-a4396/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/reference_markers.hmm OceanDNA-a4396/protein.faa > /dev/null
[2023-03-18 20:13:43,412] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:43,413] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2bc5ad87-b54e-4107-904a-352ab7d9237b/OceanDNA-a4396.fa]
[2023-03-18 20:13:43,423] [INFO] Query marker FASTA was written to OceanDNA-a4396/markers.fasta
[2023-03-18 20:13:43,423] [INFO] Task started: Blastn
[2023-03-18 20:13:43,423] [INFO] Running command: blastn -query OceanDNA-a4396/markers.fasta -db /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/reference_markers.fasta -out OceanDNA-a4396/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:43,865] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:43,865] [INFO] Selected 1 target genomes.
[2023-03-18 20:13:43,865] [INFO] Target genome list was writen to OceanDNA-a4396/target_genomes.txt
[2023-03-18 20:13:43,866] [INFO] Task started: fastANI
[2023-03-18 20:13:43,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bc5ad87-b54e-4107-904a-352ab7d9237b/OceanDNA-a4396.fa --refList OceanDNA-a4396/target_genomes.txt --output OceanDNA-a4396/fastani_result.tsv --threads 1
[2023-03-18 20:13:44,422] [INFO] Task succeeded: fastANI
[2023-03-18 20:13:44,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:13:44,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:13:44,423] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:13:44,423] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:13:44,423] [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
--------------------------------------------------------------------------------
[2023-03-18 20:13:44,423] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4396/tc_result.tsv
[2023-03-18 20:13:44,423] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:13:44,423] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:13:44,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/checkm_data
[2023-03-18 20:13:44,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:13:44,428] [INFO] Task started: CheckM
[2023-03-18 20:13:44,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4396/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4396/checkm_input OceanDNA-a4396/checkm_result
[2023-03-18 20:14:10,454] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:10,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:10,456] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:10,456] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:10,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4396/markers.fasta)
[2023-03-18 20:14:10,456] [INFO] Task started: Blastn
[2023-03-18 20:14:10,456] [INFO] Running command: blastn -query OceanDNA-a4396/markers.fasta -db /var/lib/cwl/stg83ba856b-ee47-4155-bb31-76b6ce251520/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4396/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:10,900] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:10,900] [INFO] Selected 6 target genomes.
[2023-03-18 20:14:10,901] [INFO] Target genome list was writen to OceanDNA-a4396/target_genomes_gtdb.txt
[2023-03-18 20:14:11,116] [INFO] Task started: fastANI
[2023-03-18 20:14:11,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bc5ad87-b54e-4107-904a-352ab7d9237b/OceanDNA-a4396.fa --refList OceanDNA-a4396/target_genomes_gtdb.txt --output OceanDNA-a4396/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:12,643] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:12,647] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:12,647] [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_002716085.1	s__MGIIb-O3 sp002716085	99.7643	387	404	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.47	97.47	0.87	0.87	2	conclusive
GCA_014239955.1	s__MGIIb-O3 sp014239955	76.9913	65	404	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457155.1	s__MGIIb-O3 sp002457155	76.5502	75	404	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195615.1	s__MGIIb-O3 sp004195615	76.4387	72	404	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:12,647] [INFO] GTDB search result was written to OceanDNA-a4396/result_gtdb.tsv
[2023-03-18 20:14:12,647] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:12,648] [INFO] DFAST_QC result json was written to OceanDNA-a4396/dqc_result.json
[2023-03-18 20:14:12,648] [INFO] DFAST_QC completed!
[2023-03-18 20:14:12,648] [INFO] Total running time: 0h0m40s