[2023-06-19 04:14:27,113] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:27,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:27,118] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference
[2023-06-19 04:14:28,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:28,687] [INFO] Task started: Prodigal
[2023-06-19 04:14:28,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eb89dde-d8a3-4547-bb1d-3f71fa3cfeee/GCA_018376615.1_ASM1837661v1_genomic.fna.gz | prodigal -d GCA_018376615.1_ASM1837661v1_genomic.fna/cds.fna -a GCA_018376615.1_ASM1837661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:34,255] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:34,255] [INFO] Task started: HMMsearch
[2023-06-19 04:14:34,255] [INFO] Running command: hmmsearch --tblout GCA_018376615.1_ASM1837661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/reference_markers.hmm GCA_018376615.1_ASM1837661v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:34,495] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:34,497] [INFO] Found 6/6 markers.
[2023-06-19 04:14:34,519] [INFO] Query marker FASTA was written to GCA_018376615.1_ASM1837661v1_genomic.fna/markers.fasta
[2023-06-19 04:14:34,519] [INFO] Task started: Blastn
[2023-06-19 04:14:34,520] [INFO] Running command: blastn -query GCA_018376615.1_ASM1837661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/reference_markers.fasta -out GCA_018376615.1_ASM1837661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:35,182] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:35,187] [INFO] Selected 30 target genomes.
[2023-06-19 04:14:35,187] [INFO] Target genome list was writen to GCA_018376615.1_ASM1837661v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:35,189] [INFO] Task started: fastANI
[2023-06-19 04:14:35,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb89dde-d8a3-4547-bb1d-3f71fa3cfeee/GCA_018376615.1_ASM1837661v1_genomic.fna.gz --refList GCA_018376615.1_ASM1837661v1_genomic.fna/target_genomes.txt --output GCA_018376615.1_ASM1837661v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:54,487] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:54,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:54,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:54,495] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:14:54,496] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:14:54,496] [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
--------------------------------------------------------------------------------
[2023-06-19 04:14:54,499] [INFO] DFAST Taxonomy check result was written to GCA_018376615.1_ASM1837661v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:54,500] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:54,500] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:54,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/checkm_data
[2023-06-19 04:14:54,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:54,539] [INFO] Task started: CheckM
[2023-06-19 04:14:54,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376615.1_ASM1837661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376615.1_ASM1837661v1_genomic.fna/checkm_input GCA_018376615.1_ASM1837661v1_genomic.fna/checkm_result
[2023-06-19 04:15:17,241] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:17,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:17,269] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:17,269] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:17,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376615.1_ASM1837661v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:17,270] [INFO] Task started: Blastn
[2023-06-19 04:15:17,270] [INFO] Running command: blastn -query GCA_018376615.1_ASM1837661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c9db5c-f83f-4962-aec0-a4dc31afdec0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376615.1_ASM1837661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:18,374] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:18,387] [INFO] Selected 6 target genomes.
[2023-06-19 04:15:18,387] [INFO] Target genome list was writen to GCA_018376615.1_ASM1837661v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:18,425] [INFO] Task started: fastANI
[2023-06-19 04:15:18,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb89dde-d8a3-4547-bb1d-3f71fa3cfeee/GCA_018376615.1_ASM1837661v1_genomic.fna.gz --refList GCA_018376615.1_ASM1837661v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376615.1_ASM1837661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:21,396] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:21,408] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:15:21,408] [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_003514385.1	s__CAG-177 sp003514385	96.1499	632	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	96.45	96.03	0.91	0.84	20	conclusive
GCA_002451755.1	s__CAG-177 sp002451755	94.8125	508	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	95.98	95.98	0.88	0.88	2	-
GCA_002438685.1	s__CAG-177 sp002438685	94.2174	507	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538135.1	s__CAG-177 sp003538135	89.0481	591	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.02	97.73	0.92	0.88	9	-
GCA_900770255.1	s__CAG-177 sp900770255	81.3156	417	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:15:21,410] [INFO] GTDB search result was written to GCA_018376615.1_ASM1837661v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:21,411] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:21,413] [INFO] DFAST_QC result json was written to GCA_018376615.1_ASM1837661v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:21,413] [INFO] DFAST_QC completed!
[2023-06-19 04:15:21,413] [INFO] Total running time: 0h0m54s