[2023-06-18 12:30:12,430] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:12,434] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:12,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference
[2023-06-18 12:30:14,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:14,505] [INFO] Task started: Prodigal
[2023-06-18 12:30:14,506] [INFO] Running command: gunzip -c /var/lib/cwl/stge9404ff8-148a-4c0e-9d7b-85d616b9caf3/GCA_018680045.1_ASM1868004v1_genomic.fna.gz | prodigal -d GCA_018680045.1_ASM1868004v1_genomic.fna/cds.fna -a GCA_018680045.1_ASM1868004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:30:24,842] [INFO] Task succeeded: Prodigal
[2023-06-18 12:30:24,843] [INFO] Task started: HMMsearch
[2023-06-18 12:30:24,843] [INFO] Running command: hmmsearch --tblout GCA_018680045.1_ASM1868004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/reference_markers.hmm GCA_018680045.1_ASM1868004v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:30:25,032] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:30:25,034] [INFO] Found 6/6 markers.
[2023-06-18 12:30:25,061] [INFO] Query marker FASTA was written to GCA_018680045.1_ASM1868004v1_genomic.fna/markers.fasta
[2023-06-18 12:30:25,061] [INFO] Task started: Blastn
[2023-06-18 12:30:25,061] [INFO] Running command: blastn -query GCA_018680045.1_ASM1868004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/reference_markers.fasta -out GCA_018680045.1_ASM1868004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:30:25,645] [INFO] Task succeeded: Blastn
[2023-06-18 12:30:25,650] [INFO] Selected 27 target genomes.
[2023-06-18 12:30:25,651] [INFO] Target genome list was writen to GCA_018680045.1_ASM1868004v1_genomic.fna/target_genomes.txt
[2023-06-18 12:30:25,662] [INFO] Task started: fastANI
[2023-06-18 12:30:25,662] [INFO] Running command: fastANI --query /var/lib/cwl/stge9404ff8-148a-4c0e-9d7b-85d616b9caf3/GCA_018680045.1_ASM1868004v1_genomic.fna.gz --refList GCA_018680045.1_ASM1868004v1_genomic.fna/target_genomes.txt --output GCA_018680045.1_ASM1868004v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:30:42,037] [INFO] Task succeeded: fastANI
[2023-06-18 12:30:42,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:30:42,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:30:42,044] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:30:42,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 12:30:42,044] [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
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.9019	95	559	95	below_threshold
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	76.7987	70	559	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.0049	53	559	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	75.7184	50	559	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:30:42,046] [INFO] DFAST Taxonomy check result was written to GCA_018680045.1_ASM1868004v1_genomic.fna/tc_result.tsv
[2023-06-18 12:30:42,047] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:30:42,047] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:30:42,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/checkm_data
[2023-06-18 12:30:42,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:30:42,077] [INFO] Task started: CheckM
[2023-06-18 12:30:42,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018680045.1_ASM1868004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018680045.1_ASM1868004v1_genomic.fna/checkm_input GCA_018680045.1_ASM1868004v1_genomic.fna/checkm_result
[2023-06-18 12:31:15,323] [INFO] Task succeeded: CheckM
[2023-06-18 12:31:15,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:31:15,341] [INFO] ===== Completeness check finished =====
[2023-06-18 12:31:15,342] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:31:15,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018680045.1_ASM1868004v1_genomic.fna/markers.fasta)
[2023-06-18 12:31:15,342] [INFO] Task started: Blastn
[2023-06-18 12:31:15,342] [INFO] Running command: blastn -query GCA_018680045.1_ASM1868004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd43d2750-1541-45c5-a21c-1809ce8bf1bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018680045.1_ASM1868004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:16,171] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:16,179] [INFO] Selected 27 target genomes.
[2023-06-18 12:31:16,179] [INFO] Target genome list was writen to GCA_018680045.1_ASM1868004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:31:16,219] [INFO] Task started: fastANI
[2023-06-18 12:31:16,220] [INFO] Running command: fastANI --query /var/lib/cwl/stge9404ff8-148a-4c0e-9d7b-85d616b9caf3/GCA_018680045.1_ASM1868004v1_genomic.fna.gz --refList GCA_018680045.1_ASM1868004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018680045.1_ASM1868004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:30,177] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:30,181] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 12:31:30,181] [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_009901585.1	s__R33 sp009901585	76.9019	95	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382125.1	s__Eudoraea adriatica	76.7987	70	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:31:30,185] [INFO] GTDB search result was written to GCA_018680045.1_ASM1868004v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:30,186] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:30,189] [INFO] DFAST_QC result json was written to GCA_018680045.1_ASM1868004v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:30,189] [INFO] DFAST_QC completed!
[2023-06-18 12:31:30,190] [INFO] Total running time: 0h1m18s