[2023-06-29 15:09:58,165] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:09:58,168] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:09:58,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference
[2023-06-29 15:09:59,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:09:59,375] [INFO] Task started: Prodigal
[2023-06-29 15:09:59,375] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf14e2e8-83aa-400d-b904-3e0d1fc88519/GCA_021642025.1_ASM2164202v1_genomic.fna.gz | prodigal -d GCA_021642025.1_ASM2164202v1_genomic.fna/cds.fna -a GCA_021642025.1_ASM2164202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:10:05,164] [INFO] Task succeeded: Prodigal
[2023-06-29 15:10:05,165] [INFO] Task started: HMMsearch
[2023-06-29 15:10:05,165] [INFO] Running command: hmmsearch --tblout GCA_021642025.1_ASM2164202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/reference_markers.hmm GCA_021642025.1_ASM2164202v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:10:05,442] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:10:05,444] [INFO] Found 6/6 markers.
[2023-06-29 15:10:05,469] [INFO] Query marker FASTA was written to GCA_021642025.1_ASM2164202v1_genomic.fna/markers.fasta
[2023-06-29 15:10:05,470] [INFO] Task started: Blastn
[2023-06-29 15:10:05,470] [INFO] Running command: blastn -query GCA_021642025.1_ASM2164202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/reference_markers.fasta -out GCA_021642025.1_ASM2164202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:06,195] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:06,201] [INFO] Selected 20 target genomes.
[2023-06-29 15:10:06,202] [INFO] Target genome list was writen to GCA_021642025.1_ASM2164202v1_genomic.fna/target_genomes.txt
[2023-06-29 15:10:06,204] [INFO] Task started: fastANI
[2023-06-29 15:10:06,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf14e2e8-83aa-400d-b904-3e0d1fc88519/GCA_021642025.1_ASM2164202v1_genomic.fna.gz --refList GCA_021642025.1_ASM2164202v1_genomic.fna/target_genomes.txt --output GCA_021642025.1_ASM2164202v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:18,295] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:18,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:18,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:18,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:18,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:10:18,298] [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 15:10:18,300] [INFO] DFAST Taxonomy check result was written to GCA_021642025.1_ASM2164202v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:18,301] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:18,301] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:18,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/checkm_data
[2023-06-29 15:10:18,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:18,337] [INFO] Task started: CheckM
[2023-06-29 15:10:18,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021642025.1_ASM2164202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021642025.1_ASM2164202v1_genomic.fna/checkm_input GCA_021642025.1_ASM2164202v1_genomic.fna/checkm_result
[2023-06-29 15:10:42,470] [INFO] Task succeeded: CheckM
[2023-06-29 15:10:42,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:10:42,493] [INFO] ===== Completeness check finished =====
[2023-06-29 15:10:42,493] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:10:42,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021642025.1_ASM2164202v1_genomic.fna/markers.fasta)
[2023-06-29 15:10:42,494] [INFO] Task started: Blastn
[2023-06-29 15:10:42,495] [INFO] Running command: blastn -query GCA_021642025.1_ASM2164202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f5bf574-b770-4a64-8659-a37047c91828/dqc_reference/reference_markers_gtdb.fasta -out GCA_021642025.1_ASM2164202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:43,630] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:43,633] [INFO] Selected 6 target genomes.
[2023-06-29 15:10:43,633] [INFO] Target genome list was writen to GCA_021642025.1_ASM2164202v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:10:43,634] [INFO] Task started: fastANI
[2023-06-29 15:10:43,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf14e2e8-83aa-400d-b904-3e0d1fc88519/GCA_021642025.1_ASM2164202v1_genomic.fna.gz --refList GCA_021642025.1_ASM2164202v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021642025.1_ASM2164202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:10:46,659] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:46,669] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:10:46,669] [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_003538135.1	s__CAG-177 sp003538135	97.871	643	760	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	conclusive
GCA_003514385.1	s__CAG-177 sp003514385	89.0393	591	760	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	-
GCA_002451755.1	s__CAG-177 sp002451755	87.5353	479	760	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	86.9421	502	760	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_900770255.1	s__CAG-177 sp900770255	81.0227	399	760	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	-
--------------------------------------------------------------------------------
[2023-06-29 15:10:46,672] [INFO] GTDB search result was written to GCA_021642025.1_ASM2164202v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:10:46,672] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:10:46,675] [INFO] DFAST_QC result json was written to GCA_021642025.1_ASM2164202v1_genomic.fna/dqc_result.json
[2023-06-29 15:10:46,675] [INFO] DFAST_QC completed!
[2023-06-29 15:10:46,675] [INFO] Total running time: 0h0m49s