[2023-03-18 08:42:34,374] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,375] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference
[2023-03-18 08:42:35,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,543] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,543] [INFO] Running command: cat /var/lib/cwl/stg10600590-751a-4232-9837-484c404fa86d/OceanDNA-b3139.fa | prodigal -d OceanDNA-b3139/cds.fna -a OceanDNA-b3139/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:42,315] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:42,315] [INFO] Task started: HMMsearch
[2023-03-18 08:42:42,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b3139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/reference_markers.hmm OceanDNA-b3139/protein.faa > /dev/null
[2023-03-18 08:42:42,482] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:42,483] [INFO] Found 6/6 markers.
[2023-03-18 08:42:42,492] [INFO] Query marker FASTA was written to OceanDNA-b3139/markers.fasta
[2023-03-18 08:42:42,493] [INFO] Task started: Blastn
[2023-03-18 08:42:42,494] [INFO] Running command: blastn -query OceanDNA-b3139/markers.fasta -db /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/reference_markers.fasta -out OceanDNA-b3139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:43,042] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:43,043] [INFO] Selected 27 target genomes.
[2023-03-18 08:42:43,043] [INFO] Target genome list was writen to OceanDNA-b3139/target_genomes.txt
[2023-03-18 08:42:43,061] [INFO] Task started: fastANI
[2023-03-18 08:42:43,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg10600590-751a-4232-9837-484c404fa86d/OceanDNA-b3139.fa --refList OceanDNA-b3139/target_genomes.txt --output OceanDNA-b3139/fastani_result.tsv --threads 1
[2023-03-18 08:42:55,825] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:55,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:55,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:55,826] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:55,826] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:55,826] [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
--------------------------------------------------------------------------------
[2023-03-18 08:42:55,826] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3139/tc_result.tsv
[2023-03-18 08:42:55,827] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:55,827] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:55,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/checkm_data
[2023-03-18 08:42:55,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:55,836] [INFO] Task started: CheckM
[2023-03-18 08:42:55,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3139/checkm_input OceanDNA-b3139/checkm_result
[2023-03-18 08:43:18,057] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:18,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:18,059] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:18,060] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:18,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3139/markers.fasta)
[2023-03-18 08:43:18,061] [INFO] Task started: Blastn
[2023-03-18 08:43:18,061] [INFO] Running command: blastn -query OceanDNA-b3139/markers.fasta -db /var/lib/cwl/stg1c959dc6-ff07-46f1-b5f3-24b93fcb221c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:18,939] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:18,940] [INFO] Selected 8 target genomes.
[2023-03-18 08:43:18,940] [INFO] Target genome list was writen to OceanDNA-b3139/target_genomes_gtdb.txt
[2023-03-18 08:43:18,946] [INFO] Task started: fastANI
[2023-03-18 08:43:18,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg10600590-751a-4232-9837-484c404fa86d/OceanDNA-b3139.fa --refList OceanDNA-b3139/target_genomes_gtdb.txt --output OceanDNA-b3139/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:21,204] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:21,208] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:43:21,209] [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_002346305.1	s__UBA3012 sp002346305	99.4597	321	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	95.05	95.05	0.74	0.74	2	conclusive
GCA_903902965.1	s__UBA3012 sp903902965	86.3334	304	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.39	99.39	0.86	0.86	2	-
GCA_014190175.1	s__UBA3012 sp014190175	85.4778	326	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701305.1	s__UBA3012 sp009701305	85.2389	295	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.65	99.63	0.87	0.87	3	-
GCA_009694285.1	s__UBA3012 sp009694285	84.9631	308	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031635.1	s__UBA3012 sp010031635	84.0788	284	399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:21,209] [INFO] GTDB search result was written to OceanDNA-b3139/result_gtdb.tsv
[2023-03-18 08:43:21,209] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:21,210] [INFO] DFAST_QC result json was written to OceanDNA-b3139/dqc_result.json
[2023-03-18 08:43:21,210] [INFO] DFAST_QC completed!
[2023-03-18 08:43:21,210] [INFO] Total running time: 0h0m47s