[2023-03-15 21:24:36,475] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,475] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference
[2023-03-15 21:24:37,602] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,602] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,602] [INFO] Running command: cat /var/lib/cwl/stgef293bae-ca05-4b9f-abbb-10d9bd121eb0/OceanDNA-b45827.fa | prodigal -d OceanDNA-b45827/cds.fna -a OceanDNA-b45827/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:56,391] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:56,392] [INFO] Task started: HMMsearch
[2023-03-15 21:24:56,392] [INFO] Running command: hmmsearch --tblout OceanDNA-b45827/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/reference_markers.hmm OceanDNA-b45827/protein.faa > /dev/null
[2023-03-15 21:24:56,584] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:56,585] [INFO] Found 6/6 markers.
[2023-03-15 21:24:56,609] [INFO] Query marker FASTA was written to OceanDNA-b45827/markers.fasta
[2023-03-15 21:24:56,610] [INFO] Task started: Blastn
[2023-03-15 21:24:56,611] [INFO] Running command: blastn -query OceanDNA-b45827/markers.fasta -db /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/reference_markers.fasta -out OceanDNA-b45827/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:57,177] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:57,178] [INFO] Selected 15 target genomes.
[2023-03-15 21:24:57,178] [INFO] Target genome list was writen to OceanDNA-b45827/target_genomes.txt
[2023-03-15 21:24:57,185] [INFO] Task started: fastANI
[2023-03-15 21:24:57,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgef293bae-ca05-4b9f-abbb-10d9bd121eb0/OceanDNA-b45827.fa --refList OceanDNA-b45827/target_genomes.txt --output OceanDNA-b45827/fastani_result.tsv --threads 1
[2023-03-15 21:25:09,623] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:09,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:09,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:09,624] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:09,624] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:25:09,624] [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
--------------------------------------------------------------------------------
[2023-03-15 21:25:09,624] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45827/tc_result.tsv
[2023-03-15 21:25:09,624] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:09,624] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:09,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/checkm_data
[2023-03-15 21:25:09,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:09,684] [INFO] Task started: CheckM
[2023-03-15 21:25:09,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45827/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45827/checkm_input OceanDNA-b45827/checkm_result
[2023-03-15 21:26:01,276] [INFO] Task succeeded: CheckM
[2023-03-15 21:26:01,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 21:26:01,279] [INFO] ===== Completeness check finished =====
[2023-03-15 21:26:01,279] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:26:01,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45827/markers.fasta)
[2023-03-15 21:26:01,281] [INFO] Task started: Blastn
[2023-03-15 21:26:01,281] [INFO] Running command: blastn -query OceanDNA-b45827/markers.fasta -db /var/lib/cwl/stg506543a9-4739-43a1-8725-677869fb10db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45827/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:02,236] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:02,237] [INFO] Selected 24 target genomes.
[2023-03-15 21:26:02,237] [INFO] Target genome list was writen to OceanDNA-b45827/target_genomes_gtdb.txt
[2023-03-15 21:26:02,572] [INFO] Task started: fastANI
[2023-03-15 21:26:02,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgef293bae-ca05-4b9f-abbb-10d9bd121eb0/OceanDNA-b45827.fa --refList OceanDNA-b45827/target_genomes_gtdb.txt --output OceanDNA-b45827/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:16,428] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:16,430] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:26:16,430] [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_018700525.1	s__UBA5691 sp018700525	81.6309	314	440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
--------------------------------------------------------------------------------
[2023-03-15 21:26:16,431] [INFO] GTDB search result was written to OceanDNA-b45827/result_gtdb.tsv
[2023-03-15 21:26:16,431] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:16,431] [INFO] DFAST_QC result json was written to OceanDNA-b45827/dqc_result.json
[2023-03-15 21:26:16,431] [INFO] DFAST_QC completed!
[2023-03-15 21:26:16,431] [INFO] Total running time: 0h1m40s