[2023-06-17 11:26:04,038] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:04,041] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:04,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference
[2023-06-17 11:26:05,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:05,483] [INFO] Task started: Prodigal
[2023-06-17 11:26:05,484] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfe6cf01-4e31-44bd-baa8-62c0c89412b0/GCA_009921175.1_ASM992117v1_genomic.fna.gz | prodigal -d GCA_009921175.1_ASM992117v1_genomic.fna/cds.fna -a GCA_009921175.1_ASM992117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:13,588] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:13,589] [INFO] Task started: HMMsearch
[2023-06-17 11:26:13,589] [INFO] Running command: hmmsearch --tblout GCA_009921175.1_ASM992117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/reference_markers.hmm GCA_009921175.1_ASM992117v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:13,837] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:13,838] [INFO] Found 6/6 markers.
[2023-06-17 11:26:13,860] [INFO] Query marker FASTA was written to GCA_009921175.1_ASM992117v1_genomic.fna/markers.fasta
[2023-06-17 11:26:13,860] [INFO] Task started: Blastn
[2023-06-17 11:26:13,860] [INFO] Running command: blastn -query GCA_009921175.1_ASM992117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/reference_markers.fasta -out GCA_009921175.1_ASM992117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:14,567] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:14,571] [INFO] Selected 27 target genomes.
[2023-06-17 11:26:14,571] [INFO] Target genome list was writen to GCA_009921175.1_ASM992117v1_genomic.fna/target_genomes.txt
[2023-06-17 11:26:14,603] [INFO] Task started: fastANI
[2023-06-17 11:26:14,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe6cf01-4e31-44bd-baa8-62c0c89412b0/GCA_009921175.1_ASM992117v1_genomic.fna.gz --refList GCA_009921175.1_ASM992117v1_genomic.fna/target_genomes.txt --output GCA_009921175.1_ASM992117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:26:31,311] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:31,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:26:31,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:26:31,313] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:26:31,314] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:26:31,314] [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
--------------------------------------------------------------------------------
[2023-06-17 11:26:31,316] [INFO] DFAST Taxonomy check result was written to GCA_009921175.1_ASM992117v1_genomic.fna/tc_result.tsv
[2023-06-17 11:26:31,316] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:26:31,317] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:26:31,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/checkm_data
[2023-06-17 11:26:31,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:26:31,347] [INFO] Task started: CheckM
[2023-06-17 11:26:31,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009921175.1_ASM992117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009921175.1_ASM992117v1_genomic.fna/checkm_input GCA_009921175.1_ASM992117v1_genomic.fna/checkm_result
[2023-06-17 11:27:00,096] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:00,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:00,120] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:00,120] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:00,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009921175.1_ASM992117v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:00,121] [INFO] Task started: Blastn
[2023-06-17 11:27:00,121] [INFO] Running command: blastn -query GCA_009921175.1_ASM992117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15fd2eac-fc0b-40be-9b9d-c2569057c8e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_009921175.1_ASM992117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:00,965] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:00,971] [INFO] Selected 21 target genomes.
[2023-06-17 11:27:00,971] [INFO] Target genome list was writen to GCA_009921175.1_ASM992117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:00,988] [INFO] Task started: fastANI
[2023-06-17 11:27:00,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfe6cf01-4e31-44bd-baa8-62c0c89412b0/GCA_009921175.1_ASM992117v1_genomic.fna.gz --refList GCA_009921175.1_ASM992117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009921175.1_ASM992117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:09,725] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:09,732] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:27:09,732] [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_009921175.1	s__RFYP01 sp009921175	100.0	370	375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017852395.1	s__RFYP01 sp017852395	78.536	170	375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	99.71	99.66	0.94	0.93	4	-
GCA_011526365.1	s__RFYP01 sp011526365	76.776	66	375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:09,734] [INFO] GTDB search result was written to GCA_009921175.1_ASM992117v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:09,735] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:09,738] [INFO] DFAST_QC result json was written to GCA_009921175.1_ASM992117v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:09,738] [INFO] DFAST_QC completed!
[2023-06-17 11:27:09,738] [INFO] Total running time: 0h1m6s