[2023-03-15 07:25:31,268] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference
[2023-03-15 07:25:32,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,917] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,917] [INFO] Running command: cat /var/lib/cwl/stgf573627b-76cd-440b-a14e-0bf235cbc862/OceanDNA-b1839.fa | prodigal -d OceanDNA-b1839/cds.fna -a OceanDNA-b1839/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:45,379] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:45,379] [INFO] Task started: HMMsearch
[2023-03-15 07:25:45,379] [INFO] Running command: hmmsearch --tblout OceanDNA-b1839/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/reference_markers.hmm OceanDNA-b1839/protein.faa > /dev/null
[2023-03-15 07:25:45,586] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:45,587] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf573627b-76cd-440b-a14e-0bf235cbc862/OceanDNA-b1839.fa]
[2023-03-15 07:25:45,622] [INFO] Query marker FASTA was written to OceanDNA-b1839/markers.fasta
[2023-03-15 07:25:45,624] [INFO] Task started: Blastn
[2023-03-15 07:25:45,624] [INFO] Running command: blastn -query OceanDNA-b1839/markers.fasta -db /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/reference_markers.fasta -out OceanDNA-b1839/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:46,218] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:46,226] [INFO] Selected 26 target genomes.
[2023-03-15 07:25:46,227] [INFO] Target genome list was writen to OceanDNA-b1839/target_genomes.txt
[2023-03-15 07:25:46,241] [INFO] Task started: fastANI
[2023-03-15 07:25:46,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgf573627b-76cd-440b-a14e-0bf235cbc862/OceanDNA-b1839.fa --refList OceanDNA-b1839/target_genomes.txt --output OceanDNA-b1839/fastani_result.tsv --threads 1
[2023-03-15 07:26:07,810] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:07,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:26:07,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:26:07,815] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:26:07,815] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:26:07,815] [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
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	74.8393	53	368	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	74.7218	51	368	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	74.6894	50	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:26:07,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1839/tc_result.tsv
[2023-03-15 07:26:07,823] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:26:07,823] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:26:07,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/checkm_data
[2023-03-15 07:26:07,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:26:07,900] [INFO] Task started: CheckM
[2023-03-15 07:26:07,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1839/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1839/checkm_input OceanDNA-b1839/checkm_result
[2023-03-15 07:26:42,574] [INFO] Task succeeded: CheckM
[2023-03-15 07:26:42,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:26:42,658] [INFO] ===== Completeness check finished =====
[2023-03-15 07:26:42,658] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:26:42,658] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1839/markers.fasta)
[2023-03-15 07:26:42,659] [INFO] Task started: Blastn
[2023-03-15 07:26:42,659] [INFO] Running command: blastn -query OceanDNA-b1839/markers.fasta -db /var/lib/cwl/stg66bfe9cb-5a48-43b9-83f5-3534ec0a6a2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1839/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:43,578] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:43,585] [INFO] Selected 26 target genomes.
[2023-03-15 07:26:43,585] [INFO] Target genome list was writen to OceanDNA-b1839/target_genomes_gtdb.txt
[2023-03-15 07:26:43,608] [INFO] Task started: fastANI
[2023-03-15 07:26:43,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgf573627b-76cd-440b-a14e-0bf235cbc862/OceanDNA-b1839.fa --refList OceanDNA-b1839/target_genomes_gtdb.txt --output OceanDNA-b1839/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:26:57,079] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:57,082] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:26:57,082] [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_019048865.1	s__Aquihabitans sp019048865	75.5716	53	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	75.5268	53	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	75.4995	52	368	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:26:57,084] [INFO] GTDB search result was written to OceanDNA-b1839/result_gtdb.tsv
[2023-03-15 07:26:57,088] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:26:57,092] [INFO] DFAST_QC result json was written to OceanDNA-b1839/dqc_result.json
[2023-03-15 07:26:57,092] [INFO] DFAST_QC completed!
[2023-03-15 07:26:57,092] [INFO] Total running time: 0h1m26s