[2023-03-17 08:04:06,983] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:04:06,983] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:04:06,983] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference
[2023-03-17 08:04:08,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:04:08,770] [INFO] Task started: Prodigal
[2023-03-17 08:04:08,770] [INFO] Running command: cat /var/lib/cwl/stg8aa3df48-b6a3-400d-9f5f-8ccca6e0808d/OceanDNA-b26501.fa | prodigal -d OceanDNA-b26501/cds.fna -a OceanDNA-b26501/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:04:24,728] [INFO] Task succeeded: Prodigal
[2023-03-17 08:04:24,728] [INFO] Task started: HMMsearch
[2023-03-17 08:04:24,728] [INFO] Running command: hmmsearch --tblout OceanDNA-b26501/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/reference_markers.hmm OceanDNA-b26501/protein.faa > /dev/null
[2023-03-17 08:04:24,902] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:04:24,902] [INFO] Found 6/6 markers.
[2023-03-17 08:04:24,919] [INFO] Query marker FASTA was written to OceanDNA-b26501/markers.fasta
[2023-03-17 08:04:24,920] [INFO] Task started: Blastn
[2023-03-17 08:04:24,921] [INFO] Running command: blastn -query OceanDNA-b26501/markers.fasta -db /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/reference_markers.fasta -out OceanDNA-b26501/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:04:25,539] [INFO] Task succeeded: Blastn
[2023-03-17 08:04:25,540] [INFO] Selected 30 target genomes.
[2023-03-17 08:04:25,540] [INFO] Target genome list was writen to OceanDNA-b26501/target_genomes.txt
[2023-03-17 08:04:25,556] [INFO] Task started: fastANI
[2023-03-17 08:04:25,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa3df48-b6a3-400d-9f5f-8ccca6e0808d/OceanDNA-b26501.fa --refList OceanDNA-b26501/target_genomes.txt --output OceanDNA-b26501/fastani_result.tsv --threads 1
[2023-03-17 08:04:48,760] [INFO] Task succeeded: fastANI
[2023-03-17 08:04:48,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:04:48,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:04:48,764] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:04:48,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:04:48,764] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.7377	53	816	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:04:48,765] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26501/tc_result.tsv
[2023-03-17 08:04:48,765] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:04:48,765] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:04:48,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/checkm_data
[2023-03-17 08:04:48,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:04:48,888] [INFO] Task started: CheckM
[2023-03-17 08:04:48,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26501/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26501/checkm_input OceanDNA-b26501/checkm_result
[2023-03-17 08:05:32,163] [INFO] Task succeeded: CheckM
[2023-03-17 08:05:32,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:05:32,165] [INFO] ===== Completeness check finished =====
[2023-03-17 08:05:32,165] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:05:32,165] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26501/markers.fasta)
[2023-03-17 08:05:32,167] [INFO] Task started: Blastn
[2023-03-17 08:05:32,167] [INFO] Running command: blastn -query OceanDNA-b26501/markers.fasta -db /var/lib/cwl/stgfdc7db5b-ed0d-4671-b0b3-8453cd9019bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26501/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:05:33,270] [INFO] Task succeeded: Blastn
[2023-03-17 08:05:33,271] [INFO] Selected 16 target genomes.
[2023-03-17 08:05:33,271] [INFO] Target genome list was writen to OceanDNA-b26501/target_genomes_gtdb.txt
[2023-03-17 08:05:33,882] [INFO] Task started: fastANI
[2023-03-17 08:05:33,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa3df48-b6a3-400d-9f5f-8ccca6e0808d/OceanDNA-b26501.fa --refList OceanDNA-b26501/target_genomes_gtdb.txt --output OceanDNA-b26501/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:05:41,590] [INFO] Task succeeded: fastANI
[2023-03-17 08:05:41,597] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:05:41,598] [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_016780765.1	s__UBA8309 sp016780765	98.8475	630	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	conclusive
GCA_002683535.1	s__UBA8309 sp002683535	88.2589	374	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	78.9753	318	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_002457745.1	s__UBA8309 sp002457745	78.2024	218	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	78.1389	276	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_009920665.1	s__UBA8309 sp009920665	78.0728	317	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	77.8962	282	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731315.1	s__UBA8309 sp002731315	77.8741	165	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547925.1	s__MED-G116 sp902547925	77.4231	65	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936825.1	s__UBA8309 sp009936825	77.0389	129	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.9702	129	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:05:41,598] [INFO] GTDB search result was written to OceanDNA-b26501/result_gtdb.tsv
[2023-03-17 08:05:41,598] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:05:41,599] [INFO] DFAST_QC result json was written to OceanDNA-b26501/dqc_result.json
[2023-03-17 08:05:41,599] [INFO] DFAST_QC completed!
[2023-03-17 08:05:41,599] [INFO] Total running time: 0h1m35s