[2023-03-16 20:07:31,833] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:07:31,833] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:07:31,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference
[2023-03-16 20:07:32,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:07:32,926] [INFO] Task started: Prodigal
[2023-03-16 20:07:32,926] [INFO] Running command: cat /var/lib/cwl/stg0a1fe732-61ff-4a90-9d1d-28d8bc826120/OceanDNA-b41467.fa | prodigal -d OceanDNA-b41467/cds.fna -a OceanDNA-b41467/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:07:52,790] [INFO] Task succeeded: Prodigal
[2023-03-16 20:07:52,790] [INFO] Task started: HMMsearch
[2023-03-16 20:07:52,790] [INFO] Running command: hmmsearch --tblout OceanDNA-b41467/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/reference_markers.hmm OceanDNA-b41467/protein.faa > /dev/null
[2023-03-16 20:07:52,977] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:07:52,977] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a1fe732-61ff-4a90-9d1d-28d8bc826120/OceanDNA-b41467.fa]
[2023-03-16 20:07:53,001] [INFO] Query marker FASTA was written to OceanDNA-b41467/markers.fasta
[2023-03-16 20:07:53,002] [INFO] Task started: Blastn
[2023-03-16 20:07:53,002] [INFO] Running command: blastn -query OceanDNA-b41467/markers.fasta -db /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/reference_markers.fasta -out OceanDNA-b41467/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:07:53,575] [INFO] Task succeeded: Blastn
[2023-03-16 20:07:53,578] [INFO] Selected 26 target genomes.
[2023-03-16 20:07:53,578] [INFO] Target genome list was writen to OceanDNA-b41467/target_genomes.txt
[2023-03-16 20:07:53,591] [INFO] Task started: fastANI
[2023-03-16 20:07:53,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1fe732-61ff-4a90-9d1d-28d8bc826120/OceanDNA-b41467.fa --refList OceanDNA-b41467/target_genomes.txt --output OceanDNA-b41467/fastani_result.tsv --threads 1
[2023-03-16 20:08:07,520] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:07,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:08:07,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:08:07,524] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:08:07,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:08:07,524] [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
Oceanicoccus sagamiensis	strain=NBRC 107125	GCA_002117105.1	716816	716816	type	True	77.5059	86	1157	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:08:07,526] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41467/tc_result.tsv
[2023-03-16 20:08:07,526] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:08:07,526] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:08:07,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/checkm_data
[2023-03-16 20:08:07,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:08:07,532] [INFO] Task started: CheckM
[2023-03-16 20:08:07,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41467/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41467/checkm_input OceanDNA-b41467/checkm_result
[2023-03-16 20:09:10,743] [INFO] Task succeeded: CheckM
[2023-03-16 20:09:10,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:09:10,747] [INFO] ===== Completeness check finished =====
[2023-03-16 20:09:10,747] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:09:10,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41467/markers.fasta)
[2023-03-16 20:09:10,749] [INFO] Task started: Blastn
[2023-03-16 20:09:10,749] [INFO] Running command: blastn -query OceanDNA-b41467/markers.fasta -db /var/lib/cwl/stgf6e6fd24-70a6-4a6b-b9f6-3dfd3f21ed27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41467/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:09:11,836] [INFO] Task succeeded: Blastn
[2023-03-16 20:09:11,837] [INFO] Selected 23 target genomes.
[2023-03-16 20:09:11,837] [INFO] Target genome list was writen to OceanDNA-b41467/target_genomes_gtdb.txt
[2023-03-16 20:09:11,873] [INFO] Task started: fastANI
[2023-03-16 20:09:11,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1fe732-61ff-4a90-9d1d-28d8bc826120/OceanDNA-b41467.fa --refList OceanDNA-b41467/target_genomes_gtdb.txt --output OceanDNA-b41467/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:09:27,819] [INFO] Task succeeded: fastANI
[2023-03-16 20:09:27,821] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:09:27,821] [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_000169075.1	s__Oceanicoccus sp000169075	95.8245	1082	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	98.76	98.76	0.96	0.96	2	conclusive
GCF_002117105.1	s__Oceanicoccus sagamiensis	77.542	85	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:09:27,822] [INFO] GTDB search result was written to OceanDNA-b41467/result_gtdb.tsv
[2023-03-16 20:09:27,823] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:09:27,824] [INFO] DFAST_QC result json was written to OceanDNA-b41467/dqc_result.json
[2023-03-16 20:09:27,824] [INFO] DFAST_QC completed!
[2023-03-16 20:09:27,824] [INFO] Total running time: 0h1m56s