[2023-03-16 15:26:08,855] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,855] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference
[2023-03-16 15:26:11,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:11,534] [INFO] Task started: Prodigal
[2023-03-16 15:26:11,535] [INFO] Running command: cat /var/lib/cwl/stg67dae39b-cd44-4625-8759-e1acf1860aa1/OceanDNA-b13749.fa | prodigal -d OceanDNA-b13749/cds.fna -a OceanDNA-b13749/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:18,320] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:18,320] [INFO] Task started: HMMsearch
[2023-03-16 15:26:18,320] [INFO] Running command: hmmsearch --tblout OceanDNA-b13749/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/reference_markers.hmm OceanDNA-b13749/protein.faa > /dev/null
[2023-03-16 15:26:18,576] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:18,577] [INFO] Found 6/6 markers.
[2023-03-16 15:26:18,586] [INFO] Query marker FASTA was written to OceanDNA-b13749/markers.fasta
[2023-03-16 15:26:18,586] [INFO] Task started: Blastn
[2023-03-16 15:26:18,586] [INFO] Running command: blastn -query OceanDNA-b13749/markers.fasta -db /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/reference_markers.fasta -out OceanDNA-b13749/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:20,238] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:20,239] [INFO] Selected 11 target genomes.
[2023-03-16 15:26:20,239] [INFO] Target genome list was writen to OceanDNA-b13749/target_genomes.txt
[2023-03-16 15:26:20,248] [INFO] Task started: fastANI
[2023-03-16 15:26:20,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg67dae39b-cd44-4625-8759-e1acf1860aa1/OceanDNA-b13749.fa --refList OceanDNA-b13749/target_genomes.txt --output OceanDNA-b13749/fastani_result.tsv --threads 1
[2023-03-16 15:26:26,328] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:26,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:26,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:26,329] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:26,329] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:26:26,329] [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 15:26:26,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13749/tc_result.tsv
[2023-03-16 15:26:26,330] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:26,330] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:26,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/checkm_data
[2023-03-16 15:26:26,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:26,377] [INFO] Task started: CheckM
[2023-03-16 15:26:26,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13749/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13749/checkm_input OceanDNA-b13749/checkm_result
[2023-03-16 15:26:52,449] [INFO] Task succeeded: CheckM
[2023-03-16 15:26:52,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:26:52,451] [INFO] ===== Completeness check finished =====
[2023-03-16 15:26:52,452] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:26:52,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13749/markers.fasta)
[2023-03-16 15:26:52,452] [INFO] Task started: Blastn
[2023-03-16 15:26:52,452] [INFO] Running command: blastn -query OceanDNA-b13749/markers.fasta -db /var/lib/cwl/stg24c3d341-4532-4e7a-aea4-099511837ce6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13749/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:53,384] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:53,385] [INFO] Selected 17 target genomes.
[2023-03-16 15:26:53,385] [INFO] Target genome list was writen to OceanDNA-b13749/target_genomes_gtdb.txt
[2023-03-16 15:26:54,119] [INFO] Task started: fastANI
[2023-03-16 15:26:54,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg67dae39b-cd44-4625-8759-e1acf1860aa1/OceanDNA-b13749.fa --refList OceanDNA-b13749/target_genomes_gtdb.txt --output OceanDNA-b13749/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:27:00,774] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:00,777] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:27:00,778] [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_002715665.1	s__GCA-002694895 sp002715665	92.6289	253	388	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	95.83	95.83	0.63	0.63	2	-
GCA_002711005.1	s__GCA-002694895 sp002711005	80.5048	219	388	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	95.35	95.35	0.85	0.85	2	-
GCA_002694895.1	s__GCA-002694895 sp002694895	76.8929	80	388	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009391605.1	s__GCA-002694895 sp009391605	76.5066	85	388	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-002694895;g__GCA-002694895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:27:00,778] [INFO] GTDB search result was written to OceanDNA-b13749/result_gtdb.tsv
[2023-03-16 15:27:00,778] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:27:00,779] [INFO] DFAST_QC result json was written to OceanDNA-b13749/dqc_result.json
[2023-03-16 15:27:00,779] [INFO] DFAST_QC completed!
[2023-03-16 15:27:00,779] [INFO] Total running time: 0h0m52s