[2023-03-14 14:40:53,141] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:40:53,141] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:40:53,141] [INFO] DQC Reference Directory: /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference
[2023-03-14 14:40:54,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:40:54,268] [INFO] Task started: Prodigal
[2023-03-14 14:40:54,268] [INFO] Running command: cat /var/lib/cwl/stg1299c122-e865-4812-b438-df5a6dc294e7/OceanDNA-b45224.fa | prodigal -d OceanDNA-b45224/cds.fna -a OceanDNA-b45224/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:41:27,427] [INFO] Task succeeded: Prodigal
[2023-03-14 14:41:27,427] [INFO] Task started: HMMsearch
[2023-03-14 14:41:27,427] [INFO] Running command: hmmsearch --tblout OceanDNA-b45224/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/reference_markers.hmm OceanDNA-b45224/protein.faa > /dev/null
[2023-03-14 14:41:28,021] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:41:28,022] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1299c122-e865-4812-b438-df5a6dc294e7/OceanDNA-b45224.fa]
[2023-03-14 14:41:28,110] [INFO] Query marker FASTA was written to OceanDNA-b45224/markers.fasta
[2023-03-14 14:41:28,119] [INFO] Task started: Blastn
[2023-03-14 14:41:28,120] [INFO] Running command: blastn -query OceanDNA-b45224/markers.fasta -db /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/reference_markers.fasta -out OceanDNA-b45224/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:41:29,307] [INFO] Task succeeded: Blastn
[2023-03-14 14:41:29,308] [INFO] Selected 20 target genomes.
[2023-03-14 14:41:29,308] [INFO] Target genome list was writen to OceanDNA-b45224/target_genomes.txt
[2023-03-14 14:41:29,362] [INFO] Task started: fastANI
[2023-03-14 14:41:29,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg1299c122-e865-4812-b438-df5a6dc294e7/OceanDNA-b45224.fa --refList OceanDNA-b45224/target_genomes.txt --output OceanDNA-b45224/fastani_result.tsv --threads 1
[2023-03-14 14:41:52,829] [INFO] Task succeeded: fastANI
[2023-03-14 14:41:52,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:41:52,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:41:52,845] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:41:52,846] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:41:52,846] [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
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.7276	66	1823	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	74.6951	79	1823	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	74.5657	52	1823	95	below_threshold
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	74.5376	64	1823	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:41:52,846] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45224/tc_result.tsv
[2023-03-14 14:41:52,846] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:41:52,846] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:41:52,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/checkm_data
[2023-03-14 14:41:52,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:41:52,867] [INFO] Task started: CheckM
[2023-03-14 14:41:52,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45224/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45224/checkm_input OceanDNA-b45224/checkm_result
[2023-03-14 14:43:32,148] [INFO] Task succeeded: CheckM
[2023-03-14 14:43:32,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:43:32,152] [INFO] ===== Completeness check finished =====
[2023-03-14 14:43:32,152] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:43:32,152] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45224/markers.fasta)
[2023-03-14 14:43:32,154] [INFO] Task started: Blastn
[2023-03-14 14:43:32,154] [INFO] Running command: blastn -query OceanDNA-b45224/markers.fasta -db /var/lib/cwl/stgff55cd31-c83a-4fa9-8957-2e0bffdb47d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45224/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:43:33,433] [INFO] Task succeeded: Blastn
[2023-03-14 14:43:33,433] [INFO] Selected 21 target genomes.
[2023-03-14 14:43:33,433] [INFO] Target genome list was writen to OceanDNA-b45224/target_genomes_gtdb.txt
[2023-03-14 14:43:33,447] [INFO] Task started: fastANI
[2023-03-14 14:43:33,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg1299c122-e865-4812-b438-df5a6dc294e7/OceanDNA-b45224.fa --refList OceanDNA-b45224/target_genomes_gtdb.txt --output OceanDNA-b45224/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:43:48,326] [INFO] Task succeeded: fastANI
[2023-03-14 14:43:48,330] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:43:48,330] [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
GCF_007829875.1	s__Streptomyces capillispiralis	74.6805	54	1823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017312725.1	s__Actinocatenispora sp017312725	74.5356	64	1823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:43:48,330] [INFO] GTDB search result was written to OceanDNA-b45224/result_gtdb.tsv
[2023-03-14 14:43:48,330] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:43:48,331] [INFO] DFAST_QC result json was written to OceanDNA-b45224/dqc_result.json
[2023-03-14 14:43:48,331] [INFO] DFAST_QC completed!
[2023-03-14 14:43:48,332] [INFO] Total running time: 0h2m55s