[2023-03-19 01:38:53,857] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference
[2023-03-19 01:38:54,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:54,967] [INFO] Task started: Prodigal
[2023-03-19 01:38:54,967] [INFO] Running command: cat /var/lib/cwl/stg015acba6-3a9f-49f4-b19f-7a60327402ca/OceanDNA-b13153.fa | prodigal -d OceanDNA-b13153/cds.fna -a OceanDNA-b13153/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:05,181] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:05,181] [INFO] Task started: HMMsearch
[2023-03-19 01:39:05,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b13153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/reference_markers.hmm OceanDNA-b13153/protein.faa > /dev/null
[2023-03-19 01:39:05,363] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:05,363] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg015acba6-3a9f-49f4-b19f-7a60327402ca/OceanDNA-b13153.fa]
[2023-03-19 01:39:05,387] [INFO] Query marker FASTA was written to OceanDNA-b13153/markers.fasta
[2023-03-19 01:39:05,388] [INFO] Task started: Blastn
[2023-03-19 01:39:05,388] [INFO] Running command: blastn -query OceanDNA-b13153/markers.fasta -db /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/reference_markers.fasta -out OceanDNA-b13153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:05,886] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:05,887] [INFO] Selected 18 target genomes.
[2023-03-19 01:39:05,887] [INFO] Target genome list was writen to OceanDNA-b13153/target_genomes.txt
[2023-03-19 01:39:05,922] [INFO] Task started: fastANI
[2023-03-19 01:39:05,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg015acba6-3a9f-49f4-b19f-7a60327402ca/OceanDNA-b13153.fa --refList OceanDNA-b13153/target_genomes.txt --output OceanDNA-b13153/fastani_result.tsv --threads 1
[2023-03-19 01:39:14,147] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:14,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:14,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:14,147] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:14,147] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:14,147] [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
--------------------------------------------------------------------------------
[2023-03-19 01:39:14,148] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13153/tc_result.tsv
[2023-03-19 01:39:14,148] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:14,148] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:14,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/checkm_data
[2023-03-19 01:39:14,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:14,155] [INFO] Task started: CheckM
[2023-03-19 01:39:14,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13153/checkm_input OceanDNA-b13153/checkm_result
[2023-03-19 01:39:44,717] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:44,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:44,779] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:44,779] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:44,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13153/markers.fasta)
[2023-03-19 01:39:44,780] [INFO] Task started: Blastn
[2023-03-19 01:39:44,780] [INFO] Running command: blastn -query OceanDNA-b13153/markers.fasta -db /var/lib/cwl/stg493e056f-a3fc-45a4-be63-58cb4928f37d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:45,388] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:45,389] [INFO] Selected 15 target genomes.
[2023-03-19 01:39:45,389] [INFO] Target genome list was writen to OceanDNA-b13153/target_genomes_gtdb.txt
[2023-03-19 01:39:45,458] [INFO] Task started: fastANI
[2023-03-19 01:39:45,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg015acba6-3a9f-49f4-b19f-7a60327402ca/OceanDNA-b13153.fa --refList OceanDNA-b13153/target_genomes_gtdb.txt --output OceanDNA-b13153/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:54,175] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:54,177] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:39:54,177] [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_002707495.1	s__GCA-2707495 sp002707495	77.9695	86	561	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2707495	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713145.1	s__GCA-2713145 sp002713145	77.246	55	561	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2713145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:39:54,178] [INFO] GTDB search result was written to OceanDNA-b13153/result_gtdb.tsv
[2023-03-19 01:39:54,179] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:54,180] [INFO] DFAST_QC result json was written to OceanDNA-b13153/dqc_result.json
[2023-03-19 01:39:54,180] [INFO] DFAST_QC completed!
[2023-03-19 01:39:54,180] [INFO] Total running time: 0h1m0s