[2023-03-15 08:09:45,401] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference
[2023-03-15 08:09:46,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,639] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,639] [INFO] Running command: cat /var/lib/cwl/stg8f72d3f8-34b5-4869-af43-86abc9bd0795/OceanDNA-b25912.fa | prodigal -d OceanDNA-b25912/cds.fna -a OceanDNA-b25912/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:49,376] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:49,376] [INFO] Task started: HMMsearch
[2023-03-15 08:09:49,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b25912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/reference_markers.hmm OceanDNA-b25912/protein.faa > /dev/null
[2023-03-15 08:09:49,519] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:49,520] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8f72d3f8-34b5-4869-af43-86abc9bd0795/OceanDNA-b25912.fa]
[2023-03-15 08:09:49,526] [INFO] Query marker FASTA was written to OceanDNA-b25912/markers.fasta
[2023-03-15 08:09:49,527] [INFO] Task started: Blastn
[2023-03-15 08:09:49,527] [INFO] Running command: blastn -query OceanDNA-b25912/markers.fasta -db /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/reference_markers.fasta -out OceanDNA-b25912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:50,113] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:50,114] [INFO] Selected 5 target genomes.
[2023-03-15 08:09:50,114] [INFO] Target genome list was writen to OceanDNA-b25912/target_genomes.txt
[2023-03-15 08:09:50,118] [INFO] Task started: fastANI
[2023-03-15 08:09:50,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f72d3f8-34b5-4869-af43-86abc9bd0795/OceanDNA-b25912.fa --refList OceanDNA-b25912/target_genomes.txt --output OceanDNA-b25912/fastani_result.tsv --threads 1
[2023-03-15 08:09:51,126] [INFO] Task succeeded: fastANI
[2023-03-15 08:09:51,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:09:51,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:09:51,126] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:09:51,126] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:09:51,126] [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
--------------------------------------------------------------------------------
[2023-03-15 08:09:51,127] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25912/tc_result.tsv
[2023-03-15 08:09:51,127] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:09:51,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:09:51,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/checkm_data
[2023-03-15 08:09:51,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:09:51,183] [INFO] Task started: CheckM
[2023-03-15 08:09:51,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25912/checkm_input OceanDNA-b25912/checkm_result
[2023-03-15 08:10:07,904] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:07,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.09%
Contamintation: 9.18%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:07,906] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:07,906] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:07,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25912/markers.fasta)
[2023-03-15 08:10:07,907] [INFO] Task started: Blastn
[2023-03-15 08:10:07,908] [INFO] Running command: blastn -query OceanDNA-b25912/markers.fasta -db /var/lib/cwl/stg61d3354f-2a5c-45bc-9f4c-a5a353fad7bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:08,874] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:08,875] [INFO] Selected 15 target genomes.
[2023-03-15 08:10:08,875] [INFO] Target genome list was writen to OceanDNA-b25912/target_genomes_gtdb.txt
[2023-03-15 08:10:08,886] [INFO] Task started: fastANI
[2023-03-15 08:10:08,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f72d3f8-34b5-4869-af43-86abc9bd0795/OceanDNA-b25912.fa --refList OceanDNA-b25912/target_genomes_gtdb.txt --output OceanDNA-b25912/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:11,511] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:11,517] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:10:11,517] [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_902590845.1	s__Pelagibacter_A sp902590845	90.5008	56	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653815.1	s__Pelagibacter_A sp014653815	87.184	64	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654415.1	s__Pelagibacter_A sp014654415	86.9504	64	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569785.1	s__Pelagibacter_A sp902569785	84.7219	65	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902572605.1	s__Pelagibacter_A sp902572605	84.3502	59	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	97.08	97.08	0.83	0.83	2	-
GCA_003278125.1	s__Pelagibacter_A sp003278125	83.6469	67	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	97.41	96.01	0.86	0.77	4	-
GCA_902569735.1	s__Pelagibacter_A sp902569735	83.218	54	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	95.22	95.22	0.72	0.72	2	-
GCA_902582875.1	s__Pelagibacter_A sp902582875	82.8359	62	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282965.1	s__Pelagibacter_A sp003282965	81.6362	61	89	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:11,517] [INFO] GTDB search result was written to OceanDNA-b25912/result_gtdb.tsv
[2023-03-15 08:10:11,517] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:11,518] [INFO] DFAST_QC result json was written to OceanDNA-b25912/dqc_result.json
[2023-03-15 08:10:11,518] [INFO] DFAST_QC completed!
[2023-03-15 08:10:11,518] [INFO] Total running time: 0h0m26s