[2023-03-15 16:21:34,082] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:21:34,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:21:34,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference
[2023-03-15 16:21:36,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:21:36,322] [INFO] Task started: Prodigal
[2023-03-15 16:21:36,322] [INFO] Running command: cat /var/lib/cwl/stg7716d3ba-a2b8-453e-b5ff-6f184da41930/OceanDNA-a4116.fa | prodigal -d OceanDNA-a4116/cds.fna -a OceanDNA-a4116/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:21:42,711] [INFO] Task succeeded: Prodigal
[2023-03-15 16:21:42,711] [INFO] Task started: HMMsearch
[2023-03-15 16:21:42,711] [INFO] Running command: hmmsearch --tblout OceanDNA-a4116/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/reference_markers.hmm OceanDNA-a4116/protein.faa > /dev/null
[2023-03-15 16:21:42,867] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:21:42,867] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg7716d3ba-a2b8-453e-b5ff-6f184da41930/OceanDNA-a4116.fa]
[2023-03-15 16:21:42,882] [INFO] Query marker FASTA was written to OceanDNA-a4116/markers.fasta
[2023-03-15 16:21:42,884] [INFO] Task started: Blastn
[2023-03-15 16:21:42,884] [INFO] Running command: blastn -query OceanDNA-a4116/markers.fasta -db /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/reference_markers.fasta -out OceanDNA-a4116/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:21:43,321] [INFO] Task succeeded: Blastn
[2023-03-15 16:21:43,326] [INFO] Selected 3 target genomes.
[2023-03-15 16:21:43,326] [INFO] Target genome list was writen to OceanDNA-a4116/target_genomes.txt
[2023-03-15 16:21:43,328] [INFO] Task started: fastANI
[2023-03-15 16:21:43,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg7716d3ba-a2b8-453e-b5ff-6f184da41930/OceanDNA-a4116.fa --refList OceanDNA-a4116/target_genomes.txt --output OceanDNA-a4116/fastani_result.tsv --threads 1
[2023-03-15 16:21:46,004] [INFO] Task succeeded: fastANI
[2023-03-15 16:21:46,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:21:46,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:21:46,005] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:21:46,005] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:21:46,005] [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
--------------------------------------------------------------------------------
[2023-03-15 16:21:46,008] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4116/tc_result.tsv
[2023-03-15 16:21:46,009] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:21:46,009] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:21:46,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/checkm_data
[2023-03-15 16:21:46,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:21:46,271] [INFO] Task started: CheckM
[2023-03-15 16:21:46,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4116/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4116/checkm_input OceanDNA-a4116/checkm_result
[2023-03-15 16:22:10,268] [INFO] Task succeeded: CheckM
[2023-03-15 16:22:10,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.98%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:22:10,280] [INFO] ===== Completeness check finished =====
[2023-03-15 16:22:10,280] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:22:10,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4116/markers.fasta)
[2023-03-15 16:22:10,281] [INFO] Task started: Blastn
[2023-03-15 16:22:10,281] [INFO] Running command: blastn -query OceanDNA-a4116/markers.fasta -db /var/lib/cwl/stg816b3ca3-6f8e-4f3a-9ea6-7b855dc1fcca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4116/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:22:10,701] [INFO] Task succeeded: Blastn
[2023-03-15 16:22:10,704] [INFO] Selected 7 target genomes.
[2023-03-15 16:22:10,704] [INFO] Target genome list was writen to OceanDNA-a4116/target_genomes_gtdb.txt
[2023-03-15 16:22:10,772] [INFO] Task started: fastANI
[2023-03-15 16:22:10,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg7716d3ba-a2b8-453e-b5ff-6f184da41930/OceanDNA-a4116.fa --refList OceanDNA-a4116/target_genomes_gtdb.txt --output OceanDNA-a4116/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:22:12,322] [INFO] Task succeeded: fastANI
[2023-03-15 16:22:12,324] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:22:12,324] [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_002722735.1	s__MGIIb-O3 sp002722735	90.2319	184	207	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.60	99.54	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-15 16:22:12,327] [INFO] GTDB search result was written to OceanDNA-a4116/result_gtdb.tsv
[2023-03-15 16:22:12,330] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:22:12,333] [INFO] DFAST_QC result json was written to OceanDNA-a4116/dqc_result.json
[2023-03-15 16:22:12,333] [INFO] DFAST_QC completed!
[2023-03-15 16:22:12,333] [INFO] Total running time: 0h0m38s