[2023-03-18 00:28:55,456] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,456] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference
[2023-03-18 00:28:56,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,555] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,555] [INFO] Running command: cat /var/lib/cwl/stg48cc44e2-a8a8-4690-be22-63e98c0975e1/OceanDNA-b36942.fa | prodigal -d OceanDNA-b36942/cds.fna -a OceanDNA-b36942/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:09,897] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:09,898] [INFO] Task started: HMMsearch
[2023-03-18 00:29:09,898] [INFO] Running command: hmmsearch --tblout OceanDNA-b36942/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/reference_markers.hmm OceanDNA-b36942/protein.faa > /dev/null
[2023-03-18 00:29:10,083] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:10,084] [INFO] Found 6/6 markers.
[2023-03-18 00:29:10,100] [INFO] Query marker FASTA was written to OceanDNA-b36942/markers.fasta
[2023-03-18 00:29:10,102] [INFO] Task started: Blastn
[2023-03-18 00:29:10,102] [INFO] Running command: blastn -query OceanDNA-b36942/markers.fasta -db /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/reference_markers.fasta -out OceanDNA-b36942/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:10,685] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:10,686] [INFO] Selected 35 target genomes.
[2023-03-18 00:29:10,686] [INFO] Target genome list was writen to OceanDNA-b36942/target_genomes.txt
[2023-03-18 00:29:10,723] [INFO] Task started: fastANI
[2023-03-18 00:29:10,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg48cc44e2-a8a8-4690-be22-63e98c0975e1/OceanDNA-b36942.fa --refList OceanDNA-b36942/target_genomes.txt --output OceanDNA-b36942/fastani_result.tsv --threads 1
[2023-03-18 00:29:34,297] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:34,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:34,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:34,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:29:34,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:29:34,298] [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
--------------------------------------------------------------------------------
[2023-03-18 00:29:34,298] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36942/tc_result.tsv
[2023-03-18 00:29:34,298] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:34,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:34,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/checkm_data
[2023-03-18 00:29:34,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:34,326] [INFO] Task started: CheckM
[2023-03-18 00:29:34,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36942/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36942/checkm_input OceanDNA-b36942/checkm_result
[2023-03-18 00:30:11,044] [INFO] Task succeeded: CheckM
[2023-03-18 00:30:11,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:30:11,046] [INFO] ===== Completeness check finished =====
[2023-03-18 00:30:11,047] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:30:11,047] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36942/markers.fasta)
[2023-03-18 00:30:11,048] [INFO] Task started: Blastn
[2023-03-18 00:30:11,048] [INFO] Running command: blastn -query OceanDNA-b36942/markers.fasta -db /var/lib/cwl/stgffdc45e2-eaa9-4ce3-9d79-8a620f11bea3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36942/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:30:11,969] [INFO] Task succeeded: Blastn
[2023-03-18 00:30:11,970] [INFO] Selected 14 target genomes.
[2023-03-18 00:30:11,970] [INFO] Target genome list was writen to OceanDNA-b36942/target_genomes_gtdb.txt
[2023-03-18 00:30:12,051] [INFO] Task started: fastANI
[2023-03-18 00:30:12,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg48cc44e2-a8a8-4690-be22-63e98c0975e1/OceanDNA-b36942.fa --refList OceanDNA-b36942/target_genomes_gtdb.txt --output OceanDNA-b36942/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:30:18,227] [INFO] Task succeeded: fastANI
[2023-03-18 00:30:18,233] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:30:18,233] [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_004213835.1	s__UBA4421 sp004213835	98.2696	402	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.72	97.72	0.50	0.50	2	conclusive
GCA_002726925.1	s__UBA4421 sp002726925	87.2134	437	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.34	98.19	0.75	0.72	3	-
GCA_902613475.1	s__UBA4421 sp902613475	80.9176	295	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779425.1	s__UBA4421 sp016779425	80.5458	276	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.24	97.24	0.58	0.58	2	-
GCA_902528515.1	s__UBA4421 sp902528515	79.8914	251	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731575.1	s__UBA4421 sp002731575	77.5945	130	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.29	99.29	0.71	0.71	2	-
GCA_002704225.1	s__UBA4421 sp002704225	77.4735	155	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
GCA_009936895.1	s__UBA4421 sp009936895	77.039	116	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936775.1	s__UBA4421 sp009936775	77.0009	158	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:30:18,233] [INFO] GTDB search result was written to OceanDNA-b36942/result_gtdb.tsv
[2023-03-18 00:30:18,233] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:30:18,234] [INFO] DFAST_QC result json was written to OceanDNA-b36942/dqc_result.json
[2023-03-18 00:30:18,234] [INFO] DFAST_QC completed!
[2023-03-18 00:30:18,234] [INFO] Total running time: 0h1m23s