[2023-03-17 00:17:04,520] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference
[2023-03-17 00:17:05,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,613] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,613] [INFO] Running command: cat /var/lib/cwl/stgf024fa68-ea62-46c0-8cd2-eacebf973e74/OceanDNA-b31414.fa | prodigal -d OceanDNA-b31414/cds.fna -a OceanDNA-b31414/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:13,175] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:13,176] [INFO] Task started: HMMsearch
[2023-03-17 00:17:13,176] [INFO] Running command: hmmsearch --tblout OceanDNA-b31414/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/reference_markers.hmm OceanDNA-b31414/protein.faa > /dev/null
[2023-03-17 00:17:13,326] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:13,327] [INFO] Found 6/6 markers.
[2023-03-17 00:17:13,335] [INFO] Query marker FASTA was written to OceanDNA-b31414/markers.fasta
[2023-03-17 00:17:13,336] [INFO] Task started: Blastn
[2023-03-17 00:17:13,337] [INFO] Running command: blastn -query OceanDNA-b31414/markers.fasta -db /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/reference_markers.fasta -out OceanDNA-b31414/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:13,856] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:13,856] [INFO] Selected 22 target genomes.
[2023-03-17 00:17:13,857] [INFO] Target genome list was writen to OceanDNA-b31414/target_genomes.txt
[2023-03-17 00:17:13,872] [INFO] Task started: fastANI
[2023-03-17 00:17:13,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgf024fa68-ea62-46c0-8cd2-eacebf973e74/OceanDNA-b31414.fa --refList OceanDNA-b31414/target_genomes.txt --output OceanDNA-b31414/fastani_result.tsv --threads 1
[2023-03-17 00:17:25,438] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:25,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:25,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:25,439] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:25,439] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:17:25,439] [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
--------------------------------------------------------------------------------
[2023-03-17 00:17:25,439] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31414/tc_result.tsv
[2023-03-17 00:17:25,439] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:25,439] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:25,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/checkm_data
[2023-03-17 00:17:25,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:25,507] [INFO] Task started: CheckM
[2023-03-17 00:17:25,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31414/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31414/checkm_input OceanDNA-b31414/checkm_result
[2023-03-17 00:17:50,239] [INFO] Task succeeded: CheckM
[2023-03-17 00:17:50,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:17:50,241] [INFO] ===== Completeness check finished =====
[2023-03-17 00:17:50,241] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:17:50,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31414/markers.fasta)
[2023-03-17 00:17:50,241] [INFO] Task started: Blastn
[2023-03-17 00:17:50,241] [INFO] Running command: blastn -query OceanDNA-b31414/markers.fasta -db /var/lib/cwl/stg84797e1b-f174-4b15-ac41-47bbc5593398/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31414/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:51,000] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:51,000] [INFO] Selected 13 target genomes.
[2023-03-17 00:17:51,001] [INFO] Target genome list was writen to OceanDNA-b31414/target_genomes_gtdb.txt
[2023-03-17 00:17:51,041] [INFO] Task started: fastANI
[2023-03-17 00:17:51,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgf024fa68-ea62-46c0-8cd2-eacebf973e74/OceanDNA-b31414.fa --refList OceanDNA-b31414/target_genomes_gtdb.txt --output OceanDNA-b31414/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:17:54,933] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:54,939] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:17:54,939] [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_009925685.1	s__SYAR01 sp009925685	99.6964	319	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	99.71	99.71	0.86	0.86	2	conclusive
GCA_016869775.1	s__SYAR01 sp016869775	88.2674	264	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858915.1	s__SYAR01 sp903858915	78.0512	139	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787525.1	s__SYAR01 sp005787525	77.5705	163	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959715.1	s__SYAR01 sp903959715	77.5286	136	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__SYAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190355.1	s__CAILUF01 sp014190355	76.1749	75	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__CAILUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837365.1	s__CAILUF01 sp903837365	75.9237	51	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__CAILUF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:17:54,939] [INFO] GTDB search result was written to OceanDNA-b31414/result_gtdb.tsv
[2023-03-17 00:17:54,939] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:17:54,940] [INFO] DFAST_QC result json was written to OceanDNA-b31414/dqc_result.json
[2023-03-17 00:17:54,940] [INFO] DFAST_QC completed!
[2023-03-17 00:17:54,940] [INFO] Total running time: 0h0m50s