[2023-06-29 22:19:50,284] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:19:50,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:19:50,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference
[2023-06-29 22:19:51,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:19:51,488] [INFO] Task started: Prodigal
[2023-06-29 22:19:51,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg06f64873-5b99-4179-95e0-b9bc24ad9352/GCA_016281405.1_ASM1628140v1_genomic.fna.gz | prodigal -d GCA_016281405.1_ASM1628140v1_genomic.fna/cds.fna -a GCA_016281405.1_ASM1628140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:19:54,579] [INFO] Task succeeded: Prodigal
[2023-06-29 22:19:54,580] [INFO] Task started: HMMsearch
[2023-06-29 22:19:54,580] [INFO] Running command: hmmsearch --tblout GCA_016281405.1_ASM1628140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/reference_markers.hmm GCA_016281405.1_ASM1628140v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:19:54,831] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:19:54,833] [INFO] Found 6/6 markers.
[2023-06-29 22:19:54,855] [INFO] Query marker FASTA was written to GCA_016281405.1_ASM1628140v1_genomic.fna/markers.fasta
[2023-06-29 22:19:54,855] [INFO] Task started: Blastn
[2023-06-29 22:19:54,855] [INFO] Running command: blastn -query GCA_016281405.1_ASM1628140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/reference_markers.fasta -out GCA_016281405.1_ASM1628140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:19:55,430] [INFO] Task succeeded: Blastn
[2023-06-29 22:19:55,435] [INFO] Selected 20 target genomes.
[2023-06-29 22:19:55,435] [INFO] Target genome list was writen to GCA_016281405.1_ASM1628140v1_genomic.fna/target_genomes.txt
[2023-06-29 22:19:55,437] [INFO] Task started: fastANI
[2023-06-29 22:19:55,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f64873-5b99-4179-95e0-b9bc24ad9352/GCA_016281405.1_ASM1628140v1_genomic.fna.gz --refList GCA_016281405.1_ASM1628140v1_genomic.fna/target_genomes.txt --output GCA_016281405.1_ASM1628140v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:20:09,179] [INFO] Task succeeded: fastANI
[2023-06-29 22:20:09,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:20:09,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:20:09,182] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:20:09,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:20:09,183] [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
--------------------------------------------------------------------------------
[2023-06-29 22:20:09,185] [INFO] DFAST Taxonomy check result was written to GCA_016281405.1_ASM1628140v1_genomic.fna/tc_result.tsv
[2023-06-29 22:20:09,186] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:20:09,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:20:09,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/checkm_data
[2023-06-29 22:20:09,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:20:09,214] [INFO] Task started: CheckM
[2023-06-29 22:20:09,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016281405.1_ASM1628140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016281405.1_ASM1628140v1_genomic.fna/checkm_input GCA_016281405.1_ASM1628140v1_genomic.fna/checkm_result
[2023-06-29 22:20:25,625] [INFO] Task succeeded: CheckM
[2023-06-29 22:20:25,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:20:25,646] [INFO] ===== Completeness check finished =====
[2023-06-29 22:20:25,646] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:20:25,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016281405.1_ASM1628140v1_genomic.fna/markers.fasta)
[2023-06-29 22:20:25,646] [INFO] Task started: Blastn
[2023-06-29 22:20:25,647] [INFO] Running command: blastn -query GCA_016281405.1_ASM1628140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1278e359-f41c-4ce2-bb45-24c4fd00d8df/dqc_reference/reference_markers_gtdb.fasta -out GCA_016281405.1_ASM1628140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:20:26,447] [INFO] Task succeeded: Blastn
[2023-06-29 22:20:26,452] [INFO] Selected 34 target genomes.
[2023-06-29 22:20:26,453] [INFO] Target genome list was writen to GCA_016281405.1_ASM1628140v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:20:26,518] [INFO] Task started: fastANI
[2023-06-29 22:20:26,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f64873-5b99-4179-95e0-b9bc24ad9352/GCA_016281405.1_ASM1628140v1_genomic.fna.gz --refList GCA_016281405.1_ASM1628140v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016281405.1_ASM1628140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:20:38,519] [INFO] Task succeeded: fastANI
[2023-06-29 22:20:38,526] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:20:38,527] [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_016281405.1	s__RGIG5299 sp016281405	100.0	450	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__RGIG5299;g__RGIG5299	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017504945.1	s__RGIG5299 sp017504945	77.1068	85	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__RGIG5299;g__RGIG5299	95.0	98.05	98.05	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-29 22:20:38,529] [INFO] GTDB search result was written to GCA_016281405.1_ASM1628140v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:20:38,530] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:20:38,533] [INFO] DFAST_QC result json was written to GCA_016281405.1_ASM1628140v1_genomic.fna/dqc_result.json
[2023-06-29 22:20:38,533] [INFO] DFAST_QC completed!
[2023-06-29 22:20:38,533] [INFO] Total running time: 0h0m48s