[2023-03-16 06:38:33,633] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:38:33,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:38:33,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference
[2023-03-16 06:38:37,427] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:38:37,428] [INFO] Task started: Prodigal
[2023-03-16 06:38:37,429] [INFO] Running command: cat /var/lib/cwl/stg2eba1938-49b8-42f7-a3c0-d710b8d66ad9/OceanDNA-a3777.fa | prodigal -d OceanDNA-a3777/cds.fna -a OceanDNA-a3777/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:38:44,414] [INFO] Task succeeded: Prodigal
[2023-03-16 06:38:44,414] [INFO] Task started: HMMsearch
[2023-03-16 06:38:44,414] [INFO] Running command: hmmsearch --tblout OceanDNA-a3777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/reference_markers.hmm OceanDNA-a3777/protein.faa > /dev/null
[2023-03-16 06:38:44,579] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:38:44,579] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2eba1938-49b8-42f7-a3c0-d710b8d66ad9/OceanDNA-a3777.fa]
[2023-03-16 06:38:44,587] [INFO] Query marker FASTA was written to OceanDNA-a3777/markers.fasta
[2023-03-16 06:38:44,589] [INFO] Task started: Blastn
[2023-03-16 06:38:44,589] [INFO] Running command: blastn -query OceanDNA-a3777/markers.fasta -db /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/reference_markers.fasta -out OceanDNA-a3777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:38:45,076] [INFO] Task succeeded: Blastn
[2023-03-16 06:38:45,077] [INFO] Selected 5 target genomes.
[2023-03-16 06:38:45,077] [INFO] Target genome list was writen to OceanDNA-a3777/target_genomes.txt
[2023-03-16 06:38:45,084] [INFO] Task started: fastANI
[2023-03-16 06:38:45,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eba1938-49b8-42f7-a3c0-d710b8d66ad9/OceanDNA-a3777.fa --refList OceanDNA-a3777/target_genomes.txt --output OceanDNA-a3777/fastani_result.tsv --threads 1
[2023-03-16 06:38:46,507] [INFO] Task succeeded: fastANI
[2023-03-16 06:38:46,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:38:46,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:38:46,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:38:46,508] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:38:46,508] [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
--------------------------------------------------------------------------------
[2023-03-16 06:38:46,508] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3777/tc_result.tsv
[2023-03-16 06:38:46,508] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:38:46,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:38:46,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/checkm_data
[2023-03-16 06:38:46,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:38:46,568] [INFO] Task started: CheckM
[2023-03-16 06:38:46,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3777/checkm_input OceanDNA-a3777/checkm_result
[2023-03-16 06:39:10,575] [INFO] Task succeeded: CheckM
[2023-03-16 06:39:10,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:39:10,577] [INFO] ===== Completeness check finished =====
[2023-03-16 06:39:10,577] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:39:10,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3777/markers.fasta)
[2023-03-16 06:39:10,579] [INFO] Task started: Blastn
[2023-03-16 06:39:10,579] [INFO] Running command: blastn -query OceanDNA-a3777/markers.fasta -db /var/lib/cwl/stgf43abb62-b21d-4822-972b-a21fd391faba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:39:11,135] [INFO] Task succeeded: Blastn
[2023-03-16 06:39:11,136] [INFO] Selected 7 target genomes.
[2023-03-16 06:39:11,136] [INFO] Target genome list was writen to OceanDNA-a3777/target_genomes_gtdb.txt
[2023-03-16 06:39:11,141] [INFO] Task started: fastANI
[2023-03-16 06:39:11,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eba1938-49b8-42f7-a3c0-d710b8d66ad9/OceanDNA-a3777.fa --refList OceanDNA-a3777/target_genomes_gtdb.txt --output OceanDNA-a3777/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:39:13,013] [INFO] Task succeeded: fastANI
[2023-03-16 06:39:13,016] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:39:13,016] [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_012960975.1	s__MGIIb-O2 sp004195525	95.1082	383	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.93	99.89	0.93	0.88	3	conclusive
GCA_018654845.1	s__MGIIb-O2 sp002499785	89.0145	365	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.93	99.51	0.97	0.96	15	-
--------------------------------------------------------------------------------
[2023-03-16 06:39:13,016] [INFO] GTDB search result was written to OceanDNA-a3777/result_gtdb.tsv
[2023-03-16 06:39:13,016] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:39:13,017] [INFO] DFAST_QC result json was written to OceanDNA-a3777/dqc_result.json
[2023-03-16 06:39:13,017] [INFO] DFAST_QC completed!
[2023-03-16 06:39:13,017] [INFO] Total running time: 0h0m39s