[2023-06-19 04:28:22,994] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:28:22,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:28:22,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference
[2023-06-19 04:28:25,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:28:25,246] [INFO] Task started: Prodigal
[2023-06-19 04:28:25,246] [INFO] Running command: gunzip -c /var/lib/cwl/stg73e00c83-3731-44fd-87cd-4580a04b3cd8/GCA_018268775.1_ASM1826877v1_genomic.fna.gz | prodigal -d GCA_018268775.1_ASM1826877v1_genomic.fna/cds.fna -a GCA_018268775.1_ASM1826877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:28:36,447] [INFO] Task succeeded: Prodigal
[2023-06-19 04:28:36,447] [INFO] Task started: HMMsearch
[2023-06-19 04:28:36,448] [INFO] Running command: hmmsearch --tblout GCA_018268775.1_ASM1826877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/reference_markers.hmm GCA_018268775.1_ASM1826877v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:28:36,682] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:28:36,684] [INFO] Found 6/6 markers.
[2023-06-19 04:28:36,719] [INFO] Query marker FASTA was written to GCA_018268775.1_ASM1826877v1_genomic.fna/markers.fasta
[2023-06-19 04:28:36,719] [INFO] Task started: Blastn
[2023-06-19 04:28:36,719] [INFO] Running command: blastn -query GCA_018268775.1_ASM1826877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/reference_markers.fasta -out GCA_018268775.1_ASM1826877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:28:37,407] [INFO] Task succeeded: Blastn
[2023-06-19 04:28:37,413] [INFO] Selected 12 target genomes.
[2023-06-19 04:28:37,413] [INFO] Target genome list was writen to GCA_018268775.1_ASM1826877v1_genomic.fna/target_genomes.txt
[2023-06-19 04:28:37,417] [INFO] Task started: fastANI
[2023-06-19 04:28:37,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e00c83-3731-44fd-87cd-4580a04b3cd8/GCA_018268775.1_ASM1826877v1_genomic.fna.gz --refList GCA_018268775.1_ASM1826877v1_genomic.fna/target_genomes.txt --output GCA_018268775.1_ASM1826877v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:28:49,123] [INFO] Task succeeded: fastANI
[2023-06-19 04:28:49,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:28:49,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:28:49,137] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:28:49,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:28:49,137] [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 aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	79.9996	635	1273	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	79.8258	628	1273	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	79.2573	488	1273	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.5111	327	1273	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	78.0895	330	1273	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.0841	338	1273	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.812	281	1273	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.7325	272	1273	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.7091	245	1273	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.0218	217	1273	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.0111	212	1273	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.7882	183	1273	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:28:49,139] [INFO] DFAST Taxonomy check result was written to GCA_018268775.1_ASM1826877v1_genomic.fna/tc_result.tsv
[2023-06-19 04:28:49,140] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:28:49,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:28:49,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/checkm_data
[2023-06-19 04:28:49,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:28:49,188] [INFO] Task started: CheckM
[2023-06-19 04:28:49,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018268775.1_ASM1826877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018268775.1_ASM1826877v1_genomic.fna/checkm_input GCA_018268775.1_ASM1826877v1_genomic.fna/checkm_result
[2023-06-19 04:29:24,735] [INFO] Task succeeded: CheckM
[2023-06-19 04:29:24,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:29:24,755] [INFO] ===== Completeness check finished =====
[2023-06-19 04:29:24,756] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:29:24,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018268775.1_ASM1826877v1_genomic.fna/markers.fasta)
[2023-06-19 04:29:24,757] [INFO] Task started: Blastn
[2023-06-19 04:29:24,757] [INFO] Running command: blastn -query GCA_018268775.1_ASM1826877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37310f07-03c3-4384-aa91-dc07e1ba1277/dqc_reference/reference_markers_gtdb.fasta -out GCA_018268775.1_ASM1826877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:25,814] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:25,818] [INFO] Selected 10 target genomes.
[2023-06-19 04:29:25,819] [INFO] Target genome list was writen to GCA_018268775.1_ASM1826877v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:29:25,825] [INFO] Task started: fastANI
[2023-06-19 04:29:25,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e00c83-3731-44fd-87cd-4580a04b3cd8/GCA_018268775.1_ASM1826877v1_genomic.fna.gz --refList GCA_018268775.1_ASM1826877v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018268775.1_ASM1826877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:29:35,762] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:35,774] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:29:35,774] [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_018268775.1	s__Edaphobacter sp018268775	100.0	1262	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018268895.1	s__Edaphobacter sp018268895	84.9203	1035	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	79.9893	637	1273	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	79.4389	542	1273	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	79.2529	489	1273	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	79.2054	499	1273	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	78.585	396	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	78.0911	338	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131315.1	s__Bog-209 sp003131315	76.0546	64	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-19 04:29:35,776] [INFO] GTDB search result was written to GCA_018268775.1_ASM1826877v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:29:35,777] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:29:35,781] [INFO] DFAST_QC result json was written to GCA_018268775.1_ASM1826877v1_genomic.fna/dqc_result.json
[2023-06-19 04:29:35,781] [INFO] DFAST_QC completed!
[2023-06-19 04:29:35,781] [INFO] Total running time: 0h1m13s