[2023-03-18 23:44:06,336] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference
[2023-03-18 23:44:07,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,479] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,479] [INFO] Running command: cat /var/lib/cwl/stg3469a5f3-b081-43f8-b475-1751006fc5eb/OceanDNA-b42305.fa | prodigal -d OceanDNA-b42305/cds.fna -a OceanDNA-b42305/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:11,218] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:11,218] [INFO] Task started: HMMsearch
[2023-03-18 23:44:11,218] [INFO] Running command: hmmsearch --tblout OceanDNA-b42305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/reference_markers.hmm OceanDNA-b42305/protein.faa > /dev/null
[2023-03-18 23:44:11,371] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:11,372] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3469a5f3-b081-43f8-b475-1751006fc5eb/OceanDNA-b42305.fa]
[2023-03-18 23:44:11,381] [INFO] Query marker FASTA was written to OceanDNA-b42305/markers.fasta
[2023-03-18 23:44:11,381] [INFO] Task started: Blastn
[2023-03-18 23:44:11,381] [INFO] Running command: blastn -query OceanDNA-b42305/markers.fasta -db /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/reference_markers.fasta -out OceanDNA-b42305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:11,865] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:11,866] [INFO] Selected 8 target genomes.
[2023-03-18 23:44:11,866] [INFO] Target genome list was writen to OceanDNA-b42305/target_genomes.txt
[2023-03-18 23:44:11,873] [INFO] Task started: fastANI
[2023-03-18 23:44:11,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg3469a5f3-b081-43f8-b475-1751006fc5eb/OceanDNA-b42305.fa --refList OceanDNA-b42305/target_genomes.txt --output OceanDNA-b42305/fastani_result.tsv --threads 1
[2023-03-18 23:44:14,945] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:14,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:14,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:14,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:14,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:14,946] [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 23:44:14,946] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42305/tc_result.tsv
[2023-03-18 23:44:14,946] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:14,946] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:14,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/checkm_data
[2023-03-18 23:44:14,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:14,952] [INFO] Task started: CheckM
[2023-03-18 23:44:14,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42305/checkm_input OceanDNA-b42305/checkm_result
[2023-03-18 23:44:31,202] [INFO] Task succeeded: CheckM
[2023-03-18 23:44:31,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:44:31,204] [INFO] ===== Completeness check finished =====
[2023-03-18 23:44:31,204] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:44:31,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42305/markers.fasta)
[2023-03-18 23:44:31,206] [INFO] Task started: Blastn
[2023-03-18 23:44:31,206] [INFO] Running command: blastn -query OceanDNA-b42305/markers.fasta -db /var/lib/cwl/stg80924ee6-6e92-4182-9439-773466106afa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:31,878] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:31,879] [INFO] Selected 17 target genomes.
[2023-03-18 23:44:31,879] [INFO] Target genome list was writen to OceanDNA-b42305/target_genomes_gtdb.txt
[2023-03-18 23:44:31,892] [INFO] Task started: fastANI
[2023-03-18 23:44:31,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg3469a5f3-b081-43f8-b475-1751006fc5eb/OceanDNA-b42305.fa --refList OceanDNA-b42305/target_genomes_gtdb.txt --output OceanDNA-b42305/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:44:35,638] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:35,643] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:44:35,644] [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_002710265.1	s__SAR86A sp002710265	99.017	144	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902557965.1	s__SAR86A sp902557965	82.8441	107	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_902626385.1	s__SAR86A sp902626385	77.6469	90	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000252525.1	s__SAR86A sp000252525	77.3839	79	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
GCA_902520725.1	s__SAR86A sp902520725	77.2757	54	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902516285.1	s__SAR86A sp902516285	77.0918	53	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_902617045.1	s__SAR86A sp902617045	76.4901	50	160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-18 23:44:35,644] [INFO] GTDB search result was written to OceanDNA-b42305/result_gtdb.tsv
[2023-03-18 23:44:35,644] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:44:35,645] [INFO] DFAST_QC result json was written to OceanDNA-b42305/dqc_result.json
[2023-03-18 23:44:35,645] [INFO] DFAST_QC completed!
[2023-03-18 23:44:35,645] [INFO] Total running time: 0h0m29s