[2023-03-15 05:29:12,421] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference
[2023-03-15 05:29:13,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,542] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,542] [INFO] Running command: cat /var/lib/cwl/stgf10dde42-9a78-4900-97f3-27ce68599154/OceanDNA-b22295.fa | prodigal -d OceanDNA-b22295/cds.fna -a OceanDNA-b22295/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:19,858] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:19,858] [INFO] Task started: HMMsearch
[2023-03-15 05:29:19,858] [INFO] Running command: hmmsearch --tblout OceanDNA-b22295/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/reference_markers.hmm OceanDNA-b22295/protein.faa > /dev/null
[2023-03-15 05:29:20,019] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:20,020] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf10dde42-9a78-4900-97f3-27ce68599154/OceanDNA-b22295.fa]
[2023-03-15 05:29:20,036] [INFO] Query marker FASTA was written to OceanDNA-b22295/markers.fasta
[2023-03-15 05:29:20,036] [INFO] Task started: Blastn
[2023-03-15 05:29:20,036] [INFO] Running command: blastn -query OceanDNA-b22295/markers.fasta -db /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/reference_markers.fasta -out OceanDNA-b22295/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:20,533] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:20,534] [INFO] Selected 12 target genomes.
[2023-03-15 05:29:20,534] [INFO] Target genome list was writen to OceanDNA-b22295/target_genomes.txt
[2023-03-15 05:29:20,542] [INFO] Task started: fastANI
[2023-03-15 05:29:20,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgf10dde42-9a78-4900-97f3-27ce68599154/OceanDNA-b22295.fa --refList OceanDNA-b22295/target_genomes.txt --output OceanDNA-b22295/fastani_result.tsv --threads 1
[2023-03-15 05:29:35,444] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:35,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:35,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:35,448] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:35,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:35,448] [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
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	74.6998	50	220	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	74.6588	59	220	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	74.6351	59	220	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:35,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22295/tc_result.tsv
[2023-03-15 05:29:35,448] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:35,448] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:35,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/checkm_data
[2023-03-15 05:29:35,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:35,457] [INFO] Task started: CheckM
[2023-03-15 05:29:35,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22295/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22295/checkm_input OceanDNA-b22295/checkm_result
[2023-03-15 05:29:57,379] [INFO] Task succeeded: CheckM
[2023-03-15 05:29:57,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:29:57,382] [INFO] ===== Completeness check finished =====
[2023-03-15 05:29:57,382] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:29:57,382] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22295/markers.fasta)
[2023-03-15 05:29:57,382] [INFO] Task started: Blastn
[2023-03-15 05:29:57,382] [INFO] Running command: blastn -query OceanDNA-b22295/markers.fasta -db /var/lib/cwl/stg980cd1ad-cf34-47b0-9c11-58ffa0c0a5a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22295/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:58,034] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:58,035] [INFO] Selected 15 target genomes.
[2023-03-15 05:29:58,035] [INFO] Target genome list was writen to OceanDNA-b22295/target_genomes_gtdb.txt
[2023-03-15 05:29:58,049] [INFO] Task started: fastANI
[2023-03-15 05:29:58,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgf10dde42-9a78-4900-97f3-27ce68599154/OceanDNA-b22295.fa --refList OceanDNA-b22295/target_genomes_gtdb.txt --output OceanDNA-b22295/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:09,038] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:09,040] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:09,040] [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_008086045.1	s__Nonomuraea sp008086045	74.7406	69	220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:09,040] [INFO] GTDB search result was written to OceanDNA-b22295/result_gtdb.tsv
[2023-03-15 05:30:09,041] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:09,041] [INFO] DFAST_QC result json was written to OceanDNA-b22295/dqc_result.json
[2023-03-15 05:30:09,041] [INFO] DFAST_QC completed!
[2023-03-15 05:30:09,041] [INFO] Total running time: 0h0m57s