[2023-03-18 20:13:32,794] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,795] [INFO] DQC Reference Directory: /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference
[2023-03-18 20:13:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,556] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,557] [INFO] Running command: cat /var/lib/cwl/stg2a2441cf-dae9-4199-a55f-e5ca1748581f/OceanDNA-b38369.fa | prodigal -d OceanDNA-b38369/cds.fna -a OceanDNA-b38369/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:14:12,807] [INFO] Task succeeded: Prodigal
[2023-03-18 20:14:12,808] [INFO] Task started: HMMsearch
[2023-03-18 20:14:12,808] [INFO] Running command: hmmsearch --tblout OceanDNA-b38369/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/reference_markers.hmm OceanDNA-b38369/protein.faa > /dev/null
[2023-03-18 20:14:13,097] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:14:13,097] [INFO] Found 6/6 markers.
[2023-03-18 20:14:13,132] [INFO] Query marker FASTA was written to OceanDNA-b38369/markers.fasta
[2023-03-18 20:14:13,132] [INFO] Task started: Blastn
[2023-03-18 20:14:13,132] [INFO] Running command: blastn -query OceanDNA-b38369/markers.fasta -db /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/reference_markers.fasta -out OceanDNA-b38369/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:13,761] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:13,762] [INFO] Selected 34 target genomes.
[2023-03-18 20:14:13,762] [INFO] Target genome list was writen to OceanDNA-b38369/target_genomes.txt
[2023-03-18 20:14:13,777] [INFO] Task started: fastANI
[2023-03-18 20:14:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2441cf-dae9-4199-a55f-e5ca1748581f/OceanDNA-b38369.fa --refList OceanDNA-b38369/target_genomes.txt --output OceanDNA-b38369/fastani_result.tsv --threads 1
[2023-03-18 20:14:35,345] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:35,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:35,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:35,349] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:35,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:14:35,349] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	77.0449	88	2090	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:35,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38369/tc_result.tsv
[2023-03-18 20:14:35,349] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:35,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:35,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/checkm_data
[2023-03-18 20:14:35,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:35,357] [INFO] Task started: CheckM
[2023-03-18 20:14:35,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38369/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38369/checkm_input OceanDNA-b38369/checkm_result
[2023-03-18 20:16:06,923] [INFO] Task succeeded: CheckM
[2023-03-18 20:16:06,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:16:06,927] [INFO] ===== Completeness check finished =====
[2023-03-18 20:16:06,927] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:16:06,927] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38369/markers.fasta)
[2023-03-18 20:16:06,928] [INFO] Task started: Blastn
[2023-03-18 20:16:06,928] [INFO] Running command: blastn -query OceanDNA-b38369/markers.fasta -db /var/lib/cwl/stge449c25f-783f-4596-b865-1cd1caaca8e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38369/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:16:07,963] [INFO] Task succeeded: Blastn
[2023-03-18 20:16:07,964] [INFO] Selected 34 target genomes.
[2023-03-18 20:16:07,964] [INFO] Target genome list was writen to OceanDNA-b38369/target_genomes_gtdb.txt
[2023-03-18 20:16:08,350] [INFO] Task started: fastANI
[2023-03-18 20:16:08,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2441cf-dae9-4199-a55f-e5ca1748581f/OceanDNA-b38369.fa --refList OceanDNA-b38369/target_genomes_gtdb.txt --output OceanDNA-b38369/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:16:30,970] [INFO] Task succeeded: fastANI
[2023-03-18 20:16:30,975] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:16:30,975] [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
GCF_002863865.1	s__Ketobacter alkanivorans	77.0449	88	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701845.1	s__Ketobacter sp002701845	76.6444	80	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748575.1	s__GCA-2748575 sp002748575	76.3614	96	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__GCA-2748575	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708905.1	s__Ketobacter sp002708905	76.3606	91	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785795.1	s__UBA2009 sp002335285	75.6636	53	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_013178375.1	s__Ch67 sp013178375	75.5537	84	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:16:30,975] [INFO] GTDB search result was written to OceanDNA-b38369/result_gtdb.tsv
[2023-03-18 20:16:30,976] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:16:30,976] [INFO] DFAST_QC result json was written to OceanDNA-b38369/dqc_result.json
[2023-03-18 20:16:30,976] [INFO] DFAST_QC completed!
[2023-03-18 20:16:30,976] [INFO] Total running time: 0h2m58s