[2023-03-17 08:11:32,981] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,981] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference
[2023-03-17 08:11:34,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:34,671] [INFO] Task started: Prodigal
[2023-03-17 08:11:34,671] [INFO] Running command: cat /var/lib/cwl/stge2dac14d-4ad4-4abd-bd59-74a9929aa58f/OceanDNA-b25913.fa | prodigal -d OceanDNA-b25913/cds.fna -a OceanDNA-b25913/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:38,849] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:38,849] [INFO] Task started: HMMsearch
[2023-03-17 08:11:38,849] [INFO] Running command: hmmsearch --tblout OceanDNA-b25913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/reference_markers.hmm OceanDNA-b25913/protein.faa > /dev/null
[2023-03-17 08:11:39,034] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:39,034] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge2dac14d-4ad4-4abd-bd59-74a9929aa58f/OceanDNA-b25913.fa]
[2023-03-17 08:11:39,040] [INFO] Query marker FASTA was written to OceanDNA-b25913/markers.fasta
[2023-03-17 08:11:39,042] [INFO] Task started: Blastn
[2023-03-17 08:11:39,042] [INFO] Running command: blastn -query OceanDNA-b25913/markers.fasta -db /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/reference_markers.fasta -out OceanDNA-b25913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:41,922] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:41,923] [INFO] Selected 5 target genomes.
[2023-03-17 08:11:41,923] [INFO] Target genome list was writen to OceanDNA-b25913/target_genomes.txt
[2023-03-17 08:11:41,930] [INFO] Task started: fastANI
[2023-03-17 08:11:41,930] [INFO] Running command: fastANI --query /var/lib/cwl/stge2dac14d-4ad4-4abd-bd59-74a9929aa58f/OceanDNA-b25913.fa --refList OceanDNA-b25913/target_genomes.txt --output OceanDNA-b25913/fastani_result.tsv --threads 1
[2023-03-17 08:11:44,855] [INFO] Task succeeded: fastANI
[2023-03-17 08:11:44,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:11:44,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:11:44,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:11:44,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:11:44,856] [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
--------------------------------------------------------------------------------
[2023-03-17 08:11:44,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25913/tc_result.tsv
[2023-03-17 08:11:44,857] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:11:44,857] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:11:44,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/checkm_data
[2023-03-17 08:11:44,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:11:44,869] [INFO] Task started: CheckM
[2023-03-17 08:11:44,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25913/checkm_input OceanDNA-b25913/checkm_result
[2023-03-17 08:12:04,081] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:04,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:04,083] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:04,083] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:04,083] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25913/markers.fasta)
[2023-03-17 08:12:04,085] [INFO] Task started: Blastn
[2023-03-17 08:12:04,085] [INFO] Running command: blastn -query OceanDNA-b25913/markers.fasta -db /var/lib/cwl/stg2d5ad8db-8518-4fa3-a0c9-7090d5768c38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:04,734] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:04,735] [INFO] Selected 7 target genomes.
[2023-03-17 08:12:04,735] [INFO] Target genome list was writen to OceanDNA-b25913/target_genomes_gtdb.txt
[2023-03-17 08:12:04,775] [INFO] Task started: fastANI
[2023-03-17 08:12:04,775] [INFO] Running command: fastANI --query /var/lib/cwl/stge2dac14d-4ad4-4abd-bd59-74a9929aa58f/OceanDNA-b25913.fa --refList OceanDNA-b25913/target_genomes_gtdb.txt --output OceanDNA-b25913/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:12:05,952] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:05,957] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:12:05,957] [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_902613915.1	s__Pelagibacter_A sp902613915	89.2734	184	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542795.1	s__Pelagibacter_A sp902542795	89.0751	113	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000419545.1	s__Pelagibacter_A ubique_B	88.354	194	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902545945.1	s__Pelagibacter_A sp902545945	83.1566	124	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609855.1	s__Pelagibacter_A sp902609855	82.4971	167	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457475.1	s__Pelagibacter_A sp002457475	80.835	82	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578115.1	s__GCA-2704625 sp902578115	76.0379	56	233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	95.38	95.38	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:12:05,957] [INFO] GTDB search result was written to OceanDNA-b25913/result_gtdb.tsv
[2023-03-17 08:12:05,957] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:12:05,958] [INFO] DFAST_QC result json was written to OceanDNA-b25913/dqc_result.json
[2023-03-17 08:12:05,958] [INFO] DFAST_QC completed!
[2023-03-17 08:12:05,958] [INFO] Total running time: 0h0m33s