[2023-06-16 22:23:12,391] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:23:12,393] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:23:12,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference
[2023-06-16 22:23:13,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:23:13,780] [INFO] Task started: Prodigal
[2023-06-16 22:23:13,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgd20cc816-19ea-4197-977e-fc07c788b394/GCA_013151585.1_ASM1315158v1_genomic.fna.gz | prodigal -d GCA_013151585.1_ASM1315158v1_genomic.fna/cds.fna -a GCA_013151585.1_ASM1315158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:23:29,507] [INFO] Task succeeded: Prodigal
[2023-06-16 22:23:29,508] [INFO] Task started: HMMsearch
[2023-06-16 22:23:29,508] [INFO] Running command: hmmsearch --tblout GCA_013151585.1_ASM1315158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/reference_markers.hmm GCA_013151585.1_ASM1315158v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:23:29,903] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:23:29,904] [INFO] Found 6/6 markers.
[2023-06-16 22:23:29,978] [INFO] Query marker FASTA was written to GCA_013151585.1_ASM1315158v1_genomic.fna/markers.fasta
[2023-06-16 22:23:29,979] [INFO] Task started: Blastn
[2023-06-16 22:23:29,979] [INFO] Running command: blastn -query GCA_013151585.1_ASM1315158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/reference_markers.fasta -out GCA_013151585.1_ASM1315158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:23:30,643] [INFO] Task succeeded: Blastn
[2023-06-16 22:23:30,650] [INFO] Selected 31 target genomes.
[2023-06-16 22:23:30,650] [INFO] Target genome list was writen to GCA_013151585.1_ASM1315158v1_genomic.fna/target_genomes.txt
[2023-06-16 22:23:30,663] [INFO] Task started: fastANI
[2023-06-16 22:23:30,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgd20cc816-19ea-4197-977e-fc07c788b394/GCA_013151585.1_ASM1315158v1_genomic.fna.gz --refList GCA_013151585.1_ASM1315158v1_genomic.fna/target_genomes.txt --output GCA_013151585.1_ASM1315158v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:23:58,307] [INFO] Task succeeded: fastANI
[2023-06-16 22:23:58,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:23:58,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:23:58,315] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:23:58,315] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:23:58,315] [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
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	74.9745	52	1663	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	74.9708	52	1663	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:23:58,317] [INFO] DFAST Taxonomy check result was written to GCA_013151585.1_ASM1315158v1_genomic.fna/tc_result.tsv
[2023-06-16 22:23:58,318] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:23:58,318] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:23:58,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/checkm_data
[2023-06-16 22:23:58,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:23:58,392] [INFO] Task started: CheckM
[2023-06-16 22:23:58,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013151585.1_ASM1315158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013151585.1_ASM1315158v1_genomic.fna/checkm_input GCA_013151585.1_ASM1315158v1_genomic.fna/checkm_result
[2023-06-16 22:24:43,195] [INFO] Task succeeded: CheckM
[2023-06-16 22:24:43,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:24:43,221] [INFO] ===== Completeness check finished =====
[2023-06-16 22:24:43,221] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:24:43,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013151585.1_ASM1315158v1_genomic.fna/markers.fasta)
[2023-06-16 22:24:43,222] [INFO] Task started: Blastn
[2023-06-16 22:24:43,222] [INFO] Running command: blastn -query GCA_013151585.1_ASM1315158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e8020d-627b-4a45-be7b-4cc567556f67/dqc_reference/reference_markers_gtdb.fasta -out GCA_013151585.1_ASM1315158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:24:44,014] [INFO] Task succeeded: Blastn
[2023-06-16 22:24:44,019] [INFO] Selected 29 target genomes.
[2023-06-16 22:24:44,019] [INFO] Target genome list was writen to GCA_013151585.1_ASM1315158v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:24:44,041] [INFO] Task started: fastANI
[2023-06-16 22:24:44,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgd20cc816-19ea-4197-977e-fc07c788b394/GCA_013151585.1_ASM1315158v1_genomic.fna.gz --refList GCA_013151585.1_ASM1315158v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013151585.1_ASM1315158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:25:08,018] [INFO] Task succeeded: fastANI
[2023-06-16 22:25:08,025] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:25:08,025] [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_013151585.1	s__JAADHY01 sp013151585	100.0	1629	1663	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAADHY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.1556	52	1663	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:25:08,027] [INFO] GTDB search result was written to GCA_013151585.1_ASM1315158v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:25:08,028] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:25:08,030] [INFO] DFAST_QC result json was written to GCA_013151585.1_ASM1315158v1_genomic.fna/dqc_result.json
[2023-06-16 22:25:08,031] [INFO] DFAST_QC completed!
[2023-06-16 22:25:08,031] [INFO] Total running time: 0h1m56s