[2023-03-18 22:14:42,686] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:14:42,686] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:14:42,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference
[2023-03-18 22:14:43,796] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:14:43,796] [INFO] Task started: Prodigal
[2023-03-18 22:14:43,796] [INFO] Running command: cat /var/lib/cwl/stg9584b7f8-4857-4352-8ce5-e343c4470dae/OceanDNA-b3050.fa | prodigal -d OceanDNA-b3050/cds.fna -a OceanDNA-b3050/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:14:48,717] [INFO] Task succeeded: Prodigal
[2023-03-18 22:14:48,717] [INFO] Task started: HMMsearch
[2023-03-18 22:14:48,717] [INFO] Running command: hmmsearch --tblout OceanDNA-b3050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/reference_markers.hmm OceanDNA-b3050/protein.faa > /dev/null
[2023-03-18 22:14:48,881] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:14:48,881] [INFO] Found 6/6 markers.
[2023-03-18 22:14:48,892] [INFO] Query marker FASTA was written to OceanDNA-b3050/markers.fasta
[2023-03-18 22:14:48,893] [INFO] Task started: Blastn
[2023-03-18 22:14:48,894] [INFO] Running command: blastn -query OceanDNA-b3050/markers.fasta -db /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/reference_markers.fasta -out OceanDNA-b3050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:14:49,478] [INFO] Task succeeded: Blastn
[2023-03-18 22:14:49,480] [INFO] Selected 18 target genomes.
[2023-03-18 22:14:49,480] [INFO] Target genome list was writen to OceanDNA-b3050/target_genomes.txt
[2023-03-18 22:14:49,497] [INFO] Task started: fastANI
[2023-03-18 22:14:49,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg9584b7f8-4857-4352-8ce5-e343c4470dae/OceanDNA-b3050.fa --refList OceanDNA-b3050/target_genomes.txt --output OceanDNA-b3050/fastani_result.tsv --threads 1
[2023-03-18 22:14:57,976] [INFO] Task succeeded: fastANI
[2023-03-18 22:14:57,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:14:57,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:14:57,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:14:57,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:14:57,977] [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 22:14:57,978] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3050/tc_result.tsv
[2023-03-18 22:14:57,978] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:14:57,978] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:14:57,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/checkm_data
[2023-03-18 22:14:58,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:14:58,069] [INFO] Task started: CheckM
[2023-03-18 22:14:58,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3050/checkm_input OceanDNA-b3050/checkm_result
[2023-03-18 22:15:16,849] [INFO] Task succeeded: CheckM
[2023-03-18 22:15:16,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:15:16,882] [INFO] ===== Completeness check finished =====
[2023-03-18 22:15:16,882] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:15:16,882] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3050/markers.fasta)
[2023-03-18 22:15:16,886] [INFO] Task started: Blastn
[2023-03-18 22:15:16,886] [INFO] Running command: blastn -query OceanDNA-b3050/markers.fasta -db /var/lib/cwl/stgf7b6644b-3777-47e7-9593-18b351ef7f88/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:15:17,883] [INFO] Task succeeded: Blastn
[2023-03-18 22:15:17,888] [INFO] Selected 14 target genomes.
[2023-03-18 22:15:17,888] [INFO] Target genome list was writen to OceanDNA-b3050/target_genomes_gtdb.txt
[2023-03-18 22:15:17,941] [INFO] Task started: fastANI
[2023-03-18 22:15:17,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg9584b7f8-4857-4352-8ce5-e343c4470dae/OceanDNA-b3050.fa --refList OceanDNA-b3050/target_genomes_gtdb.txt --output OceanDNA-b3050/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:15:20,618] [INFO] Task succeeded: fastANI
[2023-03-18 22:15:20,626] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:15:20,626] [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_001437855.1	s__Nanopelagicus sp001437855	99.144	209	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	96.40	95.11	0.72	0.67	12	conclusive
GCA_016870895.1	s__Nanopelagicus sp016870895	91.8633	185	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700155.1	s__Nanopelagicus sp009700155	81.7133	137	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.43	98.37	0.82	0.81	3	-
GCA_003569185.1	s__Nanopelagicus sp003569185	80.9337	130	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383815.1	s__Nanopelagicus sp000383815	80.7006	121	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030895.1	s__Nanopelagicus sp010030895	80.6521	151	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.34	97.93	0.89	0.87	8	-
GCF_002287885.2	s__Nanopelagicus limnes	80.3547	167	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897475.1	s__Nanopelagicus sp903897475	80.2939	136	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.94	98.64	0.81	0.80	6	-
GCA_016870455.1	s__Nanopelagicus sp016870455	79.9707	128	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	79.7144	149	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
GCA_016462445.1	s__Nanopelagicus sp016462445	79.2594	143	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704285.1	s__Nanopelagicus sp009704285	78.3011	69	306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:15:20,627] [INFO] GTDB search result was written to OceanDNA-b3050/result_gtdb.tsv
[2023-03-18 22:15:20,629] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:15:20,632] [INFO] DFAST_QC result json was written to OceanDNA-b3050/dqc_result.json
[2023-03-18 22:15:20,632] [INFO] DFAST_QC completed!
[2023-03-18 22:15:20,632] [INFO] Total running time: 0h0m38s