[2023-03-16 09:47:30,782] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:47:30,782] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:47:30,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference
[2023-03-16 09:47:31,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:47:31,915] [INFO] Task started: Prodigal
[2023-03-16 09:47:31,915] [INFO] Running command: cat /var/lib/cwl/stgcf25da41-6e43-4ccb-b96a-40fc266bc4c2/OceanDNA-b36279.fa | prodigal -d OceanDNA-b36279/cds.fna -a OceanDNA-b36279/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:47:39,194] [INFO] Task succeeded: Prodigal
[2023-03-16 09:47:39,194] [INFO] Task started: HMMsearch
[2023-03-16 09:47:39,194] [INFO] Running command: hmmsearch --tblout OceanDNA-b36279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/reference_markers.hmm OceanDNA-b36279/protein.faa > /dev/null
[2023-03-16 09:47:39,364] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:47:39,364] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcf25da41-6e43-4ccb-b96a-40fc266bc4c2/OceanDNA-b36279.fa]
[2023-03-16 09:47:39,382] [INFO] Query marker FASTA was written to OceanDNA-b36279/markers.fasta
[2023-03-16 09:47:39,383] [INFO] Task started: Blastn
[2023-03-16 09:47:39,383] [INFO] Running command: blastn -query OceanDNA-b36279/markers.fasta -db /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/reference_markers.fasta -out OceanDNA-b36279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:47:39,938] [INFO] Task succeeded: Blastn
[2023-03-16 09:47:39,939] [INFO] Selected 21 target genomes.
[2023-03-16 09:47:39,940] [INFO] Target genome list was writen to OceanDNA-b36279/target_genomes.txt
[2023-03-16 09:47:39,973] [INFO] Task started: fastANI
[2023-03-16 09:47:39,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf25da41-6e43-4ccb-b96a-40fc266bc4c2/OceanDNA-b36279.fa --refList OceanDNA-b36279/target_genomes.txt --output OceanDNA-b36279/fastani_result.tsv --threads 1
[2023-03-16 09:47:51,425] [INFO] Task succeeded: fastANI
[2023-03-16 09:47:51,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:47:51,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:47:51,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:47:51,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:47:51,426] [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
--------------------------------------------------------------------------------
[2023-03-16 09:47:51,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36279/tc_result.tsv
[2023-03-16 09:47:51,427] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:47:51,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:47:51,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/checkm_data
[2023-03-16 09:47:51,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:47:51,558] [INFO] Task started: CheckM
[2023-03-16 09:47:51,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36279/checkm_input OceanDNA-b36279/checkm_result
[2023-03-16 09:48:15,084] [INFO] Task succeeded: CheckM
[2023-03-16 09:48:15,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:48:15,087] [INFO] ===== Completeness check finished =====
[2023-03-16 09:48:15,087] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:48:15,087] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36279/markers.fasta)
[2023-03-16 09:48:15,088] [INFO] Task started: Blastn
[2023-03-16 09:48:15,088] [INFO] Running command: blastn -query OceanDNA-b36279/markers.fasta -db /var/lib/cwl/stg9484f15f-7971-4d89-be12-0bd87e32bfb6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:48:15,945] [INFO] Task succeeded: Blastn
[2023-03-16 09:48:15,946] [INFO] Selected 20 target genomes.
[2023-03-16 09:48:15,946] [INFO] Target genome list was writen to OceanDNA-b36279/target_genomes_gtdb.txt
[2023-03-16 09:48:16,027] [INFO] Task started: fastANI
[2023-03-16 09:48:16,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf25da41-6e43-4ccb-b96a-40fc266bc4c2/OceanDNA-b36279.fa --refList OceanDNA-b36279/target_genomes_gtdb.txt --output OceanDNA-b36279/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:48:23,517] [INFO] Task succeeded: fastANI
[2023-03-16 09:48:23,523] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:48:23,523] [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_905479985.1	s__GCA-002733105 sp905479985	78.1694	131	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646825.1	s__GCA-002733105 sp018646825	77.8391	100	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181885.1	s__GCA-002733105 sp905181885	77.4417	92	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	77.1141	88	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053005.1	s__GCA-002733105 sp011053005	76.5239	57	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.4399	56	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	76.362	62	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733715.2	s__GCA-002733105 sp002733715	76.0544	58	421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:48:23,523] [INFO] GTDB search result was written to OceanDNA-b36279/result_gtdb.tsv
[2023-03-16 09:48:23,523] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:48:23,524] [INFO] DFAST_QC result json was written to OceanDNA-b36279/dqc_result.json
[2023-03-16 09:48:23,524] [INFO] DFAST_QC completed!
[2023-03-16 09:48:23,524] [INFO] Total running time: 0h0m53s