[2024-01-25 18:14:50,654] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:50,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:50,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference
[2024-01-25 18:14:51,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:51,811] [INFO] Task started: Prodigal
[2024-01-25 18:14:51,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg153d62d1-bcb4-410c-bd58-67998bde679d/GCF_017834145.1_ASM1783414v1_genomic.fna.gz | prodigal -d GCF_017834145.1_ASM1783414v1_genomic.fna/cds.fna -a GCF_017834145.1_ASM1783414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:00,862] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:00,863] [INFO] Task started: HMMsearch
[2024-01-25 18:15:00,863] [INFO] Running command: hmmsearch --tblout GCF_017834145.1_ASM1783414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/reference_markers.hmm GCF_017834145.1_ASM1783414v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:01,060] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:01,062] [INFO] Found 6/6 markers.
[2024-01-25 18:15:01,090] [INFO] Query marker FASTA was written to GCF_017834145.1_ASM1783414v1_genomic.fna/markers.fasta
[2024-01-25 18:15:01,091] [INFO] Task started: Blastn
[2024-01-25 18:15:01,091] [INFO] Running command: blastn -query GCF_017834145.1_ASM1783414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/reference_markers.fasta -out GCF_017834145.1_ASM1783414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:01,800] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:01,802] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:01,803] [INFO] Target genome list was writen to GCF_017834145.1_ASM1783414v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:01,811] [INFO] Task started: fastANI
[2024-01-25 18:15:01,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg153d62d1-bcb4-410c-bd58-67998bde679d/GCF_017834145.1_ASM1783414v1_genomic.fna.gz --refList GCF_017834145.1_ASM1783414v1_genomic.fna/target_genomes.txt --output GCF_017834145.1_ASM1783414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:10,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:10,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:10,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:10,767] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:10,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:10,767] [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
Leucobacter exalbidus	strain=DSM 22850	GCA_017834145.1	662960	662960	type	True	100.0	1060	1060	95	conclusive
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	81.5515	548	1060	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	79.7026	412	1060	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	79.5355	393	1060	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	79.3385	397	1060	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	79.3243	399	1060	95	below_threshold
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	79.2325	404	1060	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	78.9663	315	1060	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	78.8384	303	1060	95	below_threshold
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	78.684	309	1060	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	78.2942	285	1060	95	below_threshold
Leucobacter chinensis	strain=NC76-1	GCA_019049105.1	2851010	2851010	type	True	77.925	180	1060	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	77.722	138	1060	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	76.9936	143	1060	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	76.8844	133	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:10,768] [INFO] DFAST Taxonomy check result was written to GCF_017834145.1_ASM1783414v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:10,769] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:10,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:10,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/checkm_data
[2024-01-25 18:15:10,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:10,804] [INFO] Task started: CheckM
[2024-01-25 18:15:10,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017834145.1_ASM1783414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017834145.1_ASM1783414v1_genomic.fna/checkm_input GCF_017834145.1_ASM1783414v1_genomic.fna/checkm_result
[2024-01-25 18:15:40,192] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:40,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:40,209] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:40,209] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:40,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017834145.1_ASM1783414v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:40,210] [INFO] Task started: Blastn
[2024-01-25 18:15:40,210] [INFO] Running command: blastn -query GCF_017834145.1_ASM1783414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84961488-0137-4bb2-abcf-1c859d1fc905/dqc_reference/reference_markers_gtdb.fasta -out GCF_017834145.1_ASM1783414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:41,337] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:41,340] [INFO] Selected 16 target genomes.
[2024-01-25 18:15:41,340] [INFO] Target genome list was writen to GCF_017834145.1_ASM1783414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:41,370] [INFO] Task started: fastANI
[2024-01-25 18:15:41,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg153d62d1-bcb4-410c-bd58-67998bde679d/GCF_017834145.1_ASM1783414v1_genomic.fna.gz --refList GCF_017834145.1_ASM1783414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017834145.1_ASM1783414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:51,525] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:51,535] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:51,536] [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_017834145.1	s__Leucobacter exalbidus	100.0	1059	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000350525.1	s__Leucobacter salsicius	81.5089	550	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	79.6852	415	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000421845.1	s__Leucobacter chironomi	79.5279	393	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	79.4052	355	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633415.1	s__Leucobacter sp000633415	79.3451	380	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273835.1	s__Leucobacter celer	79.3309	398	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217175.1	s__Leucobacter luti	79.2142	405	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016758255.1	s__Leucobacter chromiireducens	79.1617	349	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	79.0947	375	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	79.0704	324	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409595.1	s__Leucobacter aridicollis	78.9668	314	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.50	96.99	0.93	0.86	3	-
GCF_006716085.1	s__Leucobacter komagatae	78.9525	305	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	78.9161	335	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	78.853	375	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752355.1	s__Leucobacter sp002752355	78.8481	349	1060	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:51,537] [INFO] GTDB search result was written to GCF_017834145.1_ASM1783414v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:51,537] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:51,541] [INFO] DFAST_QC result json was written to GCF_017834145.1_ASM1783414v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:51,541] [INFO] DFAST_QC completed!
[2024-01-25 18:15:51,541] [INFO] Total running time: 0h1m1s