[2023-03-19 04:11:06,926] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stg08d494cd-0ceb-4e8a-b733-9ccafc32626f/OceanDNA-b20427.fa | prodigal -d OceanDNA-b20427/cds.fna -a OceanDNA-b20427/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:11,480] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:11,480] [INFO] Task started: HMMsearch
[2023-03-19 04:11:11,481] [INFO] Running command: hmmsearch --tblout OceanDNA-b20427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/reference_markers.hmm OceanDNA-b20427/protein.faa > /dev/null
[2023-03-19 04:11:11,733] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:11,734] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08d494cd-0ceb-4e8a-b733-9ccafc32626f/OceanDNA-b20427.fa]
[2023-03-19 04:11:11,741] [INFO] Query marker FASTA was written to OceanDNA-b20427/markers.fasta
[2023-03-19 04:11:11,743] [INFO] Task started: Blastn
[2023-03-19 04:11:11,743] [INFO] Running command: blastn -query OceanDNA-b20427/markers.fasta -db /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/reference_markers.fasta -out OceanDNA-b20427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:14,217] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:14,217] [INFO] Selected 16 target genomes.
[2023-03-19 04:11:14,218] [INFO] Target genome list was writen to OceanDNA-b20427/target_genomes.txt
[2023-03-19 04:11:14,226] [INFO] Task started: fastANI
[2023-03-19 04:11:14,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d494cd-0ceb-4e8a-b733-9ccafc32626f/OceanDNA-b20427.fa --refList OceanDNA-b20427/target_genomes.txt --output OceanDNA-b20427/fastani_result.tsv --threads 1
[2023-03-19 04:11:24,221] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:24,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:24,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:24,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:24,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:24,222] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:24,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20427/tc_result.tsv
[2023-03-19 04:11:24,222] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:24,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:24,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/checkm_data
[2023-03-19 04:11:24,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:24,232] [INFO] Task started: CheckM
[2023-03-19 04:11:24,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20427/checkm_input OceanDNA-b20427/checkm_result
[2023-03-19 04:11:38,007] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:38,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.07%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:38,009] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:38,009] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:38,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20427/markers.fasta)
[2023-03-19 04:11:38,010] [INFO] Task started: Blastn
[2023-03-19 04:11:38,010] [INFO] Running command: blastn -query OceanDNA-b20427/markers.fasta -db /var/lib/cwl/stg80e1cb1f-e696-407f-8487-5dcf29aa8697/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:38,738] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:38,739] [INFO] Selected 16 target genomes.
[2023-03-19 04:11:38,739] [INFO] Target genome list was writen to OceanDNA-b20427/target_genomes_gtdb.txt
[2023-03-19 04:11:38,983] [INFO] Task started: fastANI
[2023-03-19 04:11:38,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d494cd-0ceb-4e8a-b733-9ccafc32626f/OceanDNA-b20427.fa --refList OceanDNA-b20427/target_genomes_gtdb.txt --output OceanDNA-b20427/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:11:45,372] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:45,375] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:11:45,376] [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_012964845.1	s__D37C17 sp012964845	85.1763	106	155	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__D37C17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004124405.1	s__D37C17 sp004124405	84.6598	126	155	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__D37C17	95.0	97.83	97.40	0.76	0.68	4	-
GCA_014381415.1	s__D37C17 sp014381415	82.7016	120	155	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__D37C17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:11:45,376] [INFO] GTDB search result was written to OceanDNA-b20427/result_gtdb.tsv
[2023-03-19 04:11:45,376] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:11:45,376] [INFO] DFAST_QC result json was written to OceanDNA-b20427/dqc_result.json
[2023-03-19 04:11:45,377] [INFO] DFAST_QC completed!
[2023-03-19 04:11:45,377] [INFO] Total running time: 0h0m38s