[2024-01-25 19:47:20,820] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference
[2024-01-25 19:47:21,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,998] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,998] [INFO] Running command: gunzip -c /var/lib/cwl/stge858a1c5-c32d-42b5-b7c7-15fa95d1ec31/GCF_025264665.1_ASM2526466v1_genomic.fna.gz | prodigal -d GCF_025264665.1_ASM2526466v1_genomic.fna/cds.fna -a GCF_025264665.1_ASM2526466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:33,643] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:33,643] [INFO] Task started: HMMsearch
[2024-01-25 19:47:33,643] [INFO] Running command: hmmsearch --tblout GCF_025264665.1_ASM2526466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/reference_markers.hmm GCF_025264665.1_ASM2526466v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:33,930] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:33,931] [INFO] Found 6/6 markers.
[2024-01-25 19:47:33,968] [INFO] Query marker FASTA was written to GCF_025264665.1_ASM2526466v1_genomic.fna/markers.fasta
[2024-01-25 19:47:33,969] [INFO] Task started: Blastn
[2024-01-25 19:47:33,969] [INFO] Running command: blastn -query GCF_025264665.1_ASM2526466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/reference_markers.fasta -out GCF_025264665.1_ASM2526466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:34,594] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:34,596] [INFO] Selected 11 target genomes.
[2024-01-25 19:47:34,597] [INFO] Target genome list was writen to GCF_025264665.1_ASM2526466v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:34,614] [INFO] Task started: fastANI
[2024-01-25 19:47:34,614] [INFO] Running command: fastANI --query /var/lib/cwl/stge858a1c5-c32d-42b5-b7c7-15fa95d1ec31/GCF_025264665.1_ASM2526466v1_genomic.fna.gz --refList GCF_025264665.1_ASM2526466v1_genomic.fna/target_genomes.txt --output GCF_025264665.1_ASM2526466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:44,922] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:44,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:44,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:44,930] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:44,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:44,930] [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
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	100.0	1480	1481	95	conclusive
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	80.0311	638	1481	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.8934	481	1481	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	78.4843	311	1481	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.1205	328	1481	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.9105	301	1481	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.7858	215	1481	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.7323	245	1481	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.6837	292	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:44,937] [INFO] DFAST Taxonomy check result was written to GCF_025264665.1_ASM2526466v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:44,937] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:44,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:44,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/checkm_data
[2024-01-25 19:47:44,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:44,979] [INFO] Task started: CheckM
[2024-01-25 19:47:44,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025264665.1_ASM2526466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025264665.1_ASM2526466v1_genomic.fna/checkm_input GCF_025264665.1_ASM2526466v1_genomic.fna/checkm_result
[2024-01-25 19:48:20,732] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:20,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:20,758] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:20,758] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:20,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025264665.1_ASM2526466v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:20,760] [INFO] Task started: Blastn
[2024-01-25 19:48:20,760] [INFO] Running command: blastn -query GCF_025264665.1_ASM2526466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f418bbf-e356-469d-a02e-6cdebbf0ee94/dqc_reference/reference_markers_gtdb.fasta -out GCF_025264665.1_ASM2526466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:21,760] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:21,763] [INFO] Selected 15 target genomes.
[2024-01-25 19:48:21,763] [INFO] Target genome list was writen to GCF_025264665.1_ASM2526466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:21,775] [INFO] Task started: fastANI
[2024-01-25 19:48:21,775] [INFO] Running command: fastANI --query /var/lib/cwl/stge858a1c5-c32d-42b5-b7c7-15fa95d1ec31/GCF_025264665.1_ASM2526466v1_genomic.fna.gz --refList GCF_025264665.1_ASM2526466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025264665.1_ASM2526466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:35,696] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:35,714] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:35,714] [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_000745965.1	s__Edaphobacter aggregans	80.0314	639	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268895.1	s__Edaphobacter sp018268895	79.9506	675	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	79.867	620	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449715.1	s__Edaphobacter sp018449715	79.2123	510	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	79.0998	472	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217555.1	s__Edaphobacter modestus	78.8946	482	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688615.1	s__Edaphobacter sp000688615	78.6013	406	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274685.1	s__Edaphobacter sp014274685	78.5669	444	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093025.1	s__Edaphobacter sp010093025	78.5374	426	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897435.1	s__Edaphobacter sp001897435	77.8039	324	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_009765785.1	s__UBA5172 sp009765785	77.3471	186	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381585.1	s__KBS-83 sp000381585	77.24	108	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__KBS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289875.1	s__Silvibacterium sp013289875	76.7537	118	1481	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:35,718] [INFO] GTDB search result was written to GCF_025264665.1_ASM2526466v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:35,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:35,721] [INFO] DFAST_QC result json was written to GCF_025264665.1_ASM2526466v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:35,721] [INFO] DFAST_QC completed!
[2024-01-25 19:48:35,721] [INFO] Total running time: 0h1m15s