[2023-06-28 22:24:54,253] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:24:54,256] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:24:54,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference
[2023-06-28 22:24:55,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:24:55,632] [INFO] Task started: Prodigal
[2023-06-28 22:24:55,633] [INFO] Running command: gunzip -c /var/lib/cwl/stge831618b-e271-4925-addb-e3e5962a5749/GCA_015660765.1_ASM1566076v1_genomic.fna.gz | prodigal -d GCA_015660765.1_ASM1566076v1_genomic.fna/cds.fna -a GCA_015660765.1_ASM1566076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:25:01,171] [INFO] Task succeeded: Prodigal
[2023-06-28 22:25:01,171] [INFO] Task started: HMMsearch
[2023-06-28 22:25:01,171] [INFO] Running command: hmmsearch --tblout GCA_015660765.1_ASM1566076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/reference_markers.hmm GCA_015660765.1_ASM1566076v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:25:01,425] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:25:01,427] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge831618b-e271-4925-addb-e3e5962a5749/GCA_015660765.1_ASM1566076v1_genomic.fna.gz]
[2023-06-28 22:25:01,454] [INFO] Query marker FASTA was written to GCA_015660765.1_ASM1566076v1_genomic.fna/markers.fasta
[2023-06-28 22:25:01,454] [INFO] Task started: Blastn
[2023-06-28 22:25:01,454] [INFO] Running command: blastn -query GCA_015660765.1_ASM1566076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/reference_markers.fasta -out GCA_015660765.1_ASM1566076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:02,183] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:02,187] [INFO] Selected 24 target genomes.
[2023-06-28 22:25:02,187] [INFO] Target genome list was writen to GCA_015660765.1_ASM1566076v1_genomic.fna/target_genomes.txt
[2023-06-28 22:25:02,193] [INFO] Task started: fastANI
[2023-06-28 22:25:02,193] [INFO] Running command: fastANI --query /var/lib/cwl/stge831618b-e271-4925-addb-e3e5962a5749/GCA_015660765.1_ASM1566076v1_genomic.fna.gz --refList GCA_015660765.1_ASM1566076v1_genomic.fna/target_genomes.txt --output GCA_015660765.1_ASM1566076v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:25:22,618] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:22,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:25:22,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:25:22,629] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:25:22,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:25:22,630] [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
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.7424	53	583	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	74.7165	53	583	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	74.669	63	583	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:25:22,632] [INFO] DFAST Taxonomy check result was written to GCA_015660765.1_ASM1566076v1_genomic.fna/tc_result.tsv
[2023-06-28 22:25:22,633] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:25:22,633] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:25:22,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/checkm_data
[2023-06-28 22:25:22,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:25:22,667] [INFO] Task started: CheckM
[2023-06-28 22:25:22,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015660765.1_ASM1566076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015660765.1_ASM1566076v1_genomic.fna/checkm_input GCA_015660765.1_ASM1566076v1_genomic.fna/checkm_result
[2023-06-28 22:25:44,771] [INFO] Task succeeded: CheckM
[2023-06-28 22:25:44,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.99%
Contamintation: 5.01%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-28 22:25:44,803] [INFO] ===== Completeness check finished =====
[2023-06-28 22:25:44,803] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:25:44,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015660765.1_ASM1566076v1_genomic.fna/markers.fasta)
[2023-06-28 22:25:44,804] [INFO] Task started: Blastn
[2023-06-28 22:25:44,804] [INFO] Running command: blastn -query GCA_015660765.1_ASM1566076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg436dcdcf-ccc2-489b-93f3-45fd51dcca88/dqc_reference/reference_markers_gtdb.fasta -out GCA_015660765.1_ASM1566076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:45,974] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:45,979] [INFO] Selected 25 target genomes.
[2023-06-28 22:25:45,979] [INFO] Target genome list was writen to GCA_015660765.1_ASM1566076v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:25:45,996] [INFO] Task started: fastANI
[2023-06-28 22:25:45,997] [INFO] Running command: fastANI --query /var/lib/cwl/stge831618b-e271-4925-addb-e3e5962a5749/GCA_015660765.1_ASM1566076v1_genomic.fna.gz --refList GCA_015660765.1_ASM1566076v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015660765.1_ASM1566076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:25:58,565] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:58,575] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:25:58,575] [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_011046615.1	s__DSPQ01 sp011046615	79.9123	302	583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__E44-bin32;g__DSPQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	76.5859	54	583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789165.1	s__SpSt-583 sp016789165	75.7845	75	583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.121	63	583	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:25:58,578] [INFO] GTDB search result was written to GCA_015660765.1_ASM1566076v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:25:58,578] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:25:58,581] [INFO] DFAST_QC result json was written to GCA_015660765.1_ASM1566076v1_genomic.fna/dqc_result.json
[2023-06-28 22:25:58,582] [INFO] DFAST_QC completed!
[2023-06-28 22:25:58,582] [INFO] Total running time: 0h1m4s