[2023-03-15 04:26:44,434] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:26:44,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:26:44,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference
[2023-03-15 04:26:45,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:26:45,545] [INFO] Task started: Prodigal
[2023-03-15 04:26:45,545] [INFO] Running command: cat /var/lib/cwl/stgc1e23bf8-86ba-4203-8601-f51cc02c8d11/OceanDNA-b42265.fa | prodigal -d OceanDNA-b42265/cds.fna -a OceanDNA-b42265/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:26:47,787] [INFO] Task succeeded: Prodigal
[2023-03-15 04:26:47,787] [INFO] Task started: HMMsearch
[2023-03-15 04:26:47,787] [INFO] Running command: hmmsearch --tblout OceanDNA-b42265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/reference_markers.hmm OceanDNA-b42265/protein.faa > /dev/null
[2023-03-15 04:26:47,922] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:26:47,923] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc1e23bf8-86ba-4203-8601-f51cc02c8d11/OceanDNA-b42265.fa]
[2023-03-15 04:26:47,937] [INFO] Query marker FASTA was written to OceanDNA-b42265/markers.fasta
[2023-03-15 04:26:47,938] [INFO] Task started: Blastn
[2023-03-15 04:26:47,938] [INFO] Running command: blastn -query OceanDNA-b42265/markers.fasta -db /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/reference_markers.fasta -out OceanDNA-b42265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:26:48,426] [INFO] Task succeeded: Blastn
[2023-03-15 04:26:48,429] [INFO] Selected 6 target genomes.
[2023-03-15 04:26:48,429] [INFO] Target genome list was writen to OceanDNA-b42265/target_genomes.txt
[2023-03-15 04:26:48,433] [INFO] Task started: fastANI
[2023-03-15 04:26:48,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1e23bf8-86ba-4203-8601-f51cc02c8d11/OceanDNA-b42265.fa --refList OceanDNA-b42265/target_genomes.txt --output OceanDNA-b42265/fastani_result.tsv --threads 1
[2023-03-15 04:26:51,402] [INFO] Task succeeded: fastANI
[2023-03-15 04:26:51,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:26:51,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:26:51,403] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:26:51,403] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:26:51,403] [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 04:26:51,404] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42265/tc_result.tsv
[2023-03-15 04:26:51,406] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:26:51,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:26:51,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/checkm_data
[2023-03-15 04:26:51,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:26:51,420] [INFO] Task started: CheckM
[2023-03-15 04:26:51,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42265/checkm_input OceanDNA-b42265/checkm_result
[2023-03-15 04:27:05,144] [INFO] Task succeeded: CheckM
[2023-03-15 04:27:05,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:27:05,149] [INFO] ===== Completeness check finished =====
[2023-03-15 04:27:05,149] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:27:05,149] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42265/markers.fasta)
[2023-03-15 04:27:05,150] [INFO] Task started: Blastn
[2023-03-15 04:27:05,150] [INFO] Running command: blastn -query OceanDNA-b42265/markers.fasta -db /var/lib/cwl/stg3e968372-6db7-4382-b49b-43e56aacf30c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:27:05,958] [INFO] Task succeeded: Blastn
[2023-03-15 04:27:05,961] [INFO] Selected 14 target genomes.
[2023-03-15 04:27:05,961] [INFO] Target genome list was writen to OceanDNA-b42265/target_genomes_gtdb.txt
[2023-03-15 04:27:06,006] [INFO] Task started: fastANI
[2023-03-15 04:27:06,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1e23bf8-86ba-4203-8601-f51cc02c8d11/OceanDNA-b42265.fa --refList OceanDNA-b42265/target_genomes_gtdb.txt --output OceanDNA-b42265/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:27:08,628] [INFO] Task succeeded: fastANI
[2023-03-15 04:27:08,635] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:27:08,635] [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_902556105.1	s__SAR86A sp902556105	97.3288	114	147	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_902517505.1	s__SAR86A sp902517505	79.3962	87	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902520495.1	s__SAR86A sp902520495	78.7238	84	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721465.1	s__SAR86A sp002721465	78.4632	55	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
GCA_902559345.1	s__SAR86A sp902559345	78.4629	71	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547295.1	s__SAR86A sp902547295	78.46	74	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	78.1759	80	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_002690725.1	s__SAR86A sp002690725	78.1729	58	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_902631785.1	s__SAR86A sp902631785	77.9911	70	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902617045.1	s__SAR86A sp902617045	77.9711	82	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902630885.1	s__SAR86A sp902630885	77.9592	77	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710265.1	s__SAR86A sp002710265	77.2985	56	147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:27:08,636] [INFO] GTDB search result was written to OceanDNA-b42265/result_gtdb.tsv
[2023-03-15 04:27:08,636] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:27:08,639] [INFO] DFAST_QC result json was written to OceanDNA-b42265/dqc_result.json
[2023-03-15 04:27:08,639] [INFO] DFAST_QC completed!
[2023-03-15 04:27:08,639] [INFO] Total running time: 0h0m24s