[2024-01-24 10:57:12,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference
[2024-01-24 10:57:14,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,541] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg377325bf-a52b-4cb5-bd24-0a3fc893b1b1/GCF_016587435.1_ASM1658743v1_genomic.fna.gz | prodigal -d GCF_016587435.1_ASM1658743v1_genomic.fna/cds.fna -a GCF_016587435.1_ASM1658743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:40,109] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:40,109] [INFO] Task started: HMMsearch
[2024-01-24 10:57:40,109] [INFO] Running command: hmmsearch --tblout GCF_016587435.1_ASM1658743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/reference_markers.hmm GCF_016587435.1_ASM1658743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:40,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:40,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg377325bf-a52b-4cb5-bd24-0a3fc893b1b1/GCF_016587435.1_ASM1658743v1_genomic.fna.gz]
[2024-01-24 10:57:40,624] [INFO] Query marker FASTA was written to GCF_016587435.1_ASM1658743v1_genomic.fna/markers.fasta
[2024-01-24 10:57:40,625] [INFO] Task started: Blastn
[2024-01-24 10:57:40,625] [INFO] Running command: blastn -query GCF_016587435.1_ASM1658743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/reference_markers.fasta -out GCF_016587435.1_ASM1658743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,284] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,287] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:41,287] [INFO] Target genome list was writen to GCF_016587435.1_ASM1658743v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,292] [INFO] Task started: fastANI
[2024-01-24 10:57:41,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg377325bf-a52b-4cb5-bd24-0a3fc893b1b1/GCF_016587435.1_ASM1658743v1_genomic.fna.gz --refList GCF_016587435.1_ASM1658743v1_genomic.fna/target_genomes.txt --output GCF_016587435.1_ASM1658743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:58,275] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:58,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:58,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:58,289] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:58,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:58,290] [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
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	100.0	3031	3038	95	conclusive
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	82.3406	1723	3038	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	81.4024	1542	3038	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	80.4433	394	3038	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	79.4849	734	3038	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	78.9917	818	3038	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	78.3036	456	3038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:58,291] [INFO] DFAST Taxonomy check result was written to GCF_016587435.1_ASM1658743v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:58,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:58,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:58,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/checkm_data
[2024-01-24 10:57:58,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:58,373] [INFO] Task started: CheckM
[2024-01-24 10:57:58,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016587435.1_ASM1658743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016587435.1_ASM1658743v1_genomic.fna/checkm_input GCF_016587435.1_ASM1658743v1_genomic.fna/checkm_result
[2024-01-24 10:59:10,545] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:10,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.48%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:10,571] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:10,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:10,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016587435.1_ASM1658743v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:10,573] [INFO] Task started: Blastn
[2024-01-24 10:59:10,573] [INFO] Running command: blastn -query GCF_016587435.1_ASM1658743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a424ca6-1ac8-442a-90c3-b8bf48195b21/dqc_reference/reference_markers_gtdb.fasta -out GCF_016587435.1_ASM1658743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:11,479] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:11,482] [INFO] Selected 10 target genomes.
[2024-01-24 10:59:11,483] [INFO] Target genome list was writen to GCF_016587435.1_ASM1658743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:11,492] [INFO] Task started: fastANI
[2024-01-24 10:59:11,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg377325bf-a52b-4cb5-bd24-0a3fc893b1b1/GCF_016587435.1_ASM1658743v1_genomic.fna.gz --refList GCF_016587435.1_ASM1658743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016587435.1_ASM1658743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:27,823] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:27,837] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:27,837] [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
GCF_016587435.1	s__Dictyobacter sp016587435	100.0	3032	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003967515.1	s__Dictyobacter aurantiacus	82.3348	1726	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	81.3935	1544	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	80.434	396	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	79.4831	737	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015099395.1	s__Dictyobacter sp015099395	78.5883	366	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	78.2784	459	3038	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:27,840] [INFO] GTDB search result was written to GCF_016587435.1_ASM1658743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:27,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:27,845] [INFO] DFAST_QC result json was written to GCF_016587435.1_ASM1658743v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:27,845] [INFO] DFAST_QC completed!
[2024-01-24 10:59:27,845] [INFO] Total running time: 0h2m15s