[2023-03-18 00:05:54,501] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,501] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference
[2023-03-18 00:05:55,702] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,702] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,702] [INFO] Running command: cat /var/lib/cwl/stg53749e86-c5d9-4e74-a93a-069910b887f8/OceanDNA-b22922.fa | prodigal -d OceanDNA-b22922/cds.fna -a OceanDNA-b22922/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:27,113] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:27,114] [INFO] Task started: HMMsearch
[2023-03-18 00:06:27,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b22922/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/reference_markers.hmm OceanDNA-b22922/protein.faa > /dev/null
[2023-03-18 00:06:27,432] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:27,433] [INFO] Found 6/6 markers.
[2023-03-18 00:06:27,468] [INFO] Query marker FASTA was written to OceanDNA-b22922/markers.fasta
[2023-03-18 00:06:27,469] [INFO] Task started: Blastn
[2023-03-18 00:06:27,469] [INFO] Running command: blastn -query OceanDNA-b22922/markers.fasta -db /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/reference_markers.fasta -out OceanDNA-b22922/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:27,987] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:27,988] [INFO] Selected 17 target genomes.
[2023-03-18 00:06:27,989] [INFO] Target genome list was writen to OceanDNA-b22922/target_genomes.txt
[2023-03-18 00:06:27,998] [INFO] Task started: fastANI
[2023-03-18 00:06:27,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg53749e86-c5d9-4e74-a93a-069910b887f8/OceanDNA-b22922.fa --refList OceanDNA-b22922/target_genomes.txt --output OceanDNA-b22922/fastani_result.tsv --threads 1
[2023-03-18 00:06:42,843] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:42,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:42,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:42,848] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:42,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:06:42,848] [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
Thalassoglobus polymorphus	strain=Mal48	GCA_007744255.1	2527994	2527994	type	True	76.7977	202	1796	95	below_threshold
Thalassoglobus neptunius	strain=KOR42	GCA_007859735.1	1938619	1938619	type	True	75.759	92	1796	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:06:42,848] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22922/tc_result.tsv
[2023-03-18 00:06:42,848] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:42,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:42,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/checkm_data
[2023-03-18 00:06:42,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:42,877] [INFO] Task started: CheckM
[2023-03-18 00:06:42,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22922/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22922/checkm_input OceanDNA-b22922/checkm_result
[2023-03-18 00:08:00,897] [INFO] Task succeeded: CheckM
[2023-03-18 00:08:00,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:08:00,914] [INFO] ===== Completeness check finished =====
[2023-03-18 00:08:00,915] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:08:00,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22922/markers.fasta)
[2023-03-18 00:08:00,916] [INFO] Task started: Blastn
[2023-03-18 00:08:00,916] [INFO] Running command: blastn -query OceanDNA-b22922/markers.fasta -db /var/lib/cwl/stg479abc03-4e3f-47c5-b509-327bcac73489/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22922/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:08:01,614] [INFO] Task succeeded: Blastn
[2023-03-18 00:08:01,623] [INFO] Selected 19 target genomes.
[2023-03-18 00:08:01,623] [INFO] Target genome list was writen to OceanDNA-b22922/target_genomes_gtdb.txt
[2023-03-18 00:08:01,639] [INFO] Task started: fastANI
[2023-03-18 00:08:01,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg53749e86-c5d9-4e74-a93a-069910b887f8/OceanDNA-b22922.fa --refList OceanDNA-b22922/target_genomes_gtdb.txt --output OceanDNA-b22922/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:08:14,643] [INFO] Task succeeded: fastANI
[2023-03-18 00:08:14,646] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:08:14,646] [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_018659505.1	s__Thalassoglobus sp018659505	98.9483	954	1796	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007744255.1	s__Thalassoglobus polymorphus	76.7746	204	1796	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859735.1	s__Thalassoglobus neptunius	75.759	92	1796	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:08:14,650] [INFO] GTDB search result was written to OceanDNA-b22922/result_gtdb.tsv
[2023-03-18 00:08:14,650] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:08:14,654] [INFO] DFAST_QC result json was written to OceanDNA-b22922/dqc_result.json
[2023-03-18 00:08:14,654] [INFO] DFAST_QC completed!
[2023-03-18 00:08:14,654] [INFO] Total running time: 0h2m20s