[2023-06-13 10:22:12,894] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:22:12,897] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:22:12,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference
[2023-06-13 10:22:16,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:22:16,388] [INFO] Task started: Prodigal
[2023-06-13 10:22:16,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f97634b-4065-4693-94c4-1b2c7547ec2e/GCA_022708625.1_ASM2270862v1_genomic.fna.gz | prodigal -d GCA_022708625.1_ASM2270862v1_genomic.fna/cds.fna -a GCA_022708625.1_ASM2270862v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:22:32,554] [INFO] Task succeeded: Prodigal
[2023-06-13 10:22:32,556] [INFO] Task started: HMMsearch
[2023-06-13 10:22:32,556] [INFO] Running command: hmmsearch --tblout GCA_022708625.1_ASM2270862v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/reference_markers.hmm GCA_022708625.1_ASM2270862v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:22:32,884] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:22:32,886] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f97634b-4065-4693-94c4-1b2c7547ec2e/GCA_022708625.1_ASM2270862v1_genomic.fna.gz]
[2023-06-13 10:22:32,930] [INFO] Query marker FASTA was written to GCA_022708625.1_ASM2270862v1_genomic.fna/markers.fasta
[2023-06-13 10:22:32,930] [INFO] Task started: Blastn
[2023-06-13 10:22:32,930] [INFO] Running command: blastn -query GCA_022708625.1_ASM2270862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/reference_markers.fasta -out GCA_022708625.1_ASM2270862v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:22:33,592] [INFO] Task succeeded: Blastn
[2023-06-13 10:22:33,596] [INFO] Selected 21 target genomes.
[2023-06-13 10:22:33,597] [INFO] Target genome list was writen to GCA_022708625.1_ASM2270862v1_genomic.fna/target_genomes.txt
[2023-06-13 10:22:33,602] [INFO] Task started: fastANI
[2023-06-13 10:22:33,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f97634b-4065-4693-94c4-1b2c7547ec2e/GCA_022708625.1_ASM2270862v1_genomic.fna.gz --refList GCA_022708625.1_ASM2270862v1_genomic.fna/target_genomes.txt --output GCA_022708625.1_ASM2270862v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:22:48,871] [INFO] Task succeeded: fastANI
[2023-06-13 10:22:48,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:22:48,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:22:48,879] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:22:48,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:22:48,879] [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
Perlabentimonas gracilis	strain=M08_MB	GCA_011174675.1	2715279	2715279	type	True	76.2344	73	994	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:22:48,885] [INFO] DFAST Taxonomy check result was written to GCA_022708625.1_ASM2270862v1_genomic.fna/tc_result.tsv
[2023-06-13 10:22:48,886] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:22:48,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:22:48,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/checkm_data
[2023-06-13 10:22:48,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:22:48,924] [INFO] Task started: CheckM
[2023-06-13 10:22:48,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708625.1_ASM2270862v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708625.1_ASM2270862v1_genomic.fna/checkm_input GCA_022708625.1_ASM2270862v1_genomic.fna/checkm_result
[2023-06-13 10:23:36,972] [INFO] Task succeeded: CheckM
[2023-06-13 10:23:36,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:23:36,995] [INFO] ===== Completeness check finished =====
[2023-06-13 10:23:36,995] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:23:36,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708625.1_ASM2270862v1_genomic.fna/markers.fasta)
[2023-06-13 10:23:36,996] [INFO] Task started: Blastn
[2023-06-13 10:23:36,996] [INFO] Running command: blastn -query GCA_022708625.1_ASM2270862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce5b5d45-d0fb-4f4a-8233-844bf7680b66/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708625.1_ASM2270862v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:23:37,891] [INFO] Task succeeded: Blastn
[2023-06-13 10:23:37,896] [INFO] Selected 24 target genomes.
[2023-06-13 10:23:37,897] [INFO] Target genome list was writen to GCA_022708625.1_ASM2270862v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:23:37,935] [INFO] Task started: fastANI
[2023-06-13 10:23:37,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f97634b-4065-4693-94c4-1b2c7547ec2e/GCA_022708625.1_ASM2270862v1_genomic.fna.gz --refList GCA_022708625.1_ASM2270862v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708625.1_ASM2270862v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:23:50,504] [INFO] Task succeeded: fastANI
[2023-06-13 10:23:50,511] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:23:50,511] [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_002071445.1	s__MWFE01 sp002071445	99.947	932	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__MWFE01	95.0	99.90	99.83	0.96	0.93	9	conclusive
GCA_011174675.1	s__UBA5261 sp011174675	76.2344	73	994	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tenuifilaceae;g__UBA5261	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:23:50,514] [INFO] GTDB search result was written to GCA_022708625.1_ASM2270862v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:23:50,515] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:23:50,517] [INFO] DFAST_QC result json was written to GCA_022708625.1_ASM2270862v1_genomic.fna/dqc_result.json
[2023-06-13 10:23:50,518] [INFO] DFAST_QC completed!
[2023-06-13 10:23:50,518] [INFO] Total running time: 0h1m38s