[2023-03-16 03:47:32,863] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference
[2023-03-16 03:47:34,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,482] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,482] [INFO] Running command: cat /var/lib/cwl/stg56a9b189-8502-4766-8b31-8cab1f3e14e0/OceanDNA-b46091.fa | prodigal -d OceanDNA-b46091/cds.fna -a OceanDNA-b46091/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:50,487] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:50,488] [INFO] Task started: HMMsearch
[2023-03-16 03:47:50,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b46091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/reference_markers.hmm OceanDNA-b46091/protein.faa > /dev/null
[2023-03-16 03:47:50,653] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:50,654] [INFO] Found 6/6 markers.
[2023-03-16 03:47:50,667] [INFO] Query marker FASTA was written to OceanDNA-b46091/markers.fasta
[2023-03-16 03:47:50,667] [INFO] Task started: Blastn
[2023-03-16 03:47:50,667] [INFO] Running command: blastn -query OceanDNA-b46091/markers.fasta -db /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/reference_markers.fasta -out OceanDNA-b46091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:51,238] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:51,239] [INFO] Selected 21 target genomes.
[2023-03-16 03:47:51,239] [INFO] Target genome list was writen to OceanDNA-b46091/target_genomes.txt
[2023-03-16 03:47:51,249] [INFO] Task started: fastANI
[2023-03-16 03:47:51,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a9b189-8502-4766-8b31-8cab1f3e14e0/OceanDNA-b46091.fa --refList OceanDNA-b46091/target_genomes.txt --output OceanDNA-b46091/fastani_result.tsv --threads 1
[2023-03-16 03:48:03,814] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:03,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:03,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:03,818] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:03,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:03,818] [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
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	76.2797	63	655	95	below_threshold
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.0802	56	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:03,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46091/tc_result.tsv
[2023-03-16 03:48:03,819] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:03,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:03,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/checkm_data
[2023-03-16 03:48:03,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:03,823] [INFO] Task started: CheckM
[2023-03-16 03:48:03,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46091/checkm_input OceanDNA-b46091/checkm_result
[2023-03-16 03:48:46,813] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:46,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:46,816] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:46,816] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:46,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46091/markers.fasta)
[2023-03-16 03:48:46,816] [INFO] Task started: Blastn
[2023-03-16 03:48:46,816] [INFO] Running command: blastn -query OceanDNA-b46091/markers.fasta -db /var/lib/cwl/stg6fd5cb7a-1ecd-4c23-8e6a-b9d292202aac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:47,766] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:47,766] [INFO] Selected 23 target genomes.
[2023-03-16 03:48:47,767] [INFO] Target genome list was writen to OceanDNA-b46091/target_genomes_gtdb.txt
[2023-03-16 03:48:47,828] [INFO] Task started: fastANI
[2023-03-16 03:48:47,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a9b189-8502-4766-8b31-8cab1f3e14e0/OceanDNA-b46091.fa --refList OceanDNA-b46091/target_genomes_gtdb.txt --output OceanDNA-b46091/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:59,116] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:59,119] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:48:59,119] [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_002469895.1	s__Coraliomargarita sp002469895	99.6729	579	655	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	99.42	99.21	0.91	0.88	4	conclusive
GCF_000025905.1	s__Coraliomargarita akajimensis	76.2797	63	655	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185655.1	s__WN38 sp003185655	76.0802	56	655	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:59,119] [INFO] GTDB search result was written to OceanDNA-b46091/result_gtdb.tsv
[2023-03-16 03:48:59,119] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:59,120] [INFO] DFAST_QC result json was written to OceanDNA-b46091/dqc_result.json
[2023-03-16 03:48:59,120] [INFO] DFAST_QC completed!
[2023-03-16 03:48:59,120] [INFO] Total running time: 0h1m26s