[2024-01-24 13:19:01,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference
[2024-01-24 13:19:02,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,778] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg01c5c718-3a9e-46fd-8f12-10192f12b615/GCF_008831155.1_ASM883115v1_genomic.fna.gz | prodigal -d GCF_008831155.1_ASM883115v1_genomic.fna/cds.fna -a GCF_008831155.1_ASM883115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:13,110] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:13,110] [INFO] Task started: HMMsearch
[2024-01-24 13:19:13,110] [INFO] Running command: hmmsearch --tblout GCF_008831155.1_ASM883115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/reference_markers.hmm GCF_008831155.1_ASM883115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:13,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:13,480] [INFO] Found 6/6 markers.
[2024-01-24 13:19:13,515] [INFO] Query marker FASTA was written to GCF_008831155.1_ASM883115v1_genomic.fna/markers.fasta
[2024-01-24 13:19:13,515] [INFO] Task started: Blastn
[2024-01-24 13:19:13,515] [INFO] Running command: blastn -query GCF_008831155.1_ASM883115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/reference_markers.fasta -out GCF_008831155.1_ASM883115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:14,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:14,404] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:14,404] [INFO] Target genome list was writen to GCF_008831155.1_ASM883115v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:14,416] [INFO] Task started: fastANI
[2024-01-24 13:19:14,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c5c718-3a9e-46fd-8f12-10192f12b615/GCF_008831155.1_ASM883115v1_genomic.fna.gz --refList GCF_008831155.1_ASM883115v1_genomic.fna/target_genomes.txt --output GCF_008831155.1_ASM883115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:23,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:23,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:23,240] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:23,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:23,241] [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
Gulosibacter chungangensis	strain=KCTC 13959	GCA_008831155.1	979746	979746	type	True	100.0	1068	1069	95	conclusive
Gulosibacter molinativorax	strain=DSM 13485	GCA_000425685.1	256821	256821	type	True	81.1526	501	1069	95	below_threshold
Gulosibacter molinativorax	strain=ON4	GCA_003010915.2	256821	256821	type	True	81.1213	529	1069	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	78.3497	263	1069	95	below_threshold
Gulosibacter macacae	strain=YIM 102482-1	GCA_003865375.1	2488791	2488791	type	True	78.2357	239	1069	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	77.3289	100	1069	95	below_threshold
Mycetocola lacteus	strain=JCM 11654	GCA_003667575.1	76637	76637	type	True	77.301	88	1069	95	below_threshold
Microbacterium luteum	strain=A18JL200	GCA_015277875.1	2782167	2782167	type	True	77.1082	120	1069	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	77.1045	112	1069	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	76.7317	120	1069	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	76.6264	121	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:23,242] [INFO] DFAST Taxonomy check result was written to GCF_008831155.1_ASM883115v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:23,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:23,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:23,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/checkm_data
[2024-01-24 13:19:23,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:23,294] [INFO] Task started: CheckM
[2024-01-24 13:19:23,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008831155.1_ASM883115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008831155.1_ASM883115v1_genomic.fna/checkm_input GCF_008831155.1_ASM883115v1_genomic.fna/checkm_result
[2024-01-24 13:19:58,196] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:58,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,211] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:58,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:58,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008831155.1_ASM883115v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:58,212] [INFO] Task started: Blastn
[2024-01-24 13:19:58,213] [INFO] Running command: blastn -query GCF_008831155.1_ASM883115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c6620f-e17a-43f7-b252-836ac47f5baf/dqc_reference/reference_markers_gtdb.fasta -out GCF_008831155.1_ASM883115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:59,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:59,406] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:59,406] [INFO] Target genome list was writen to GCF_008831155.1_ASM883115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:59,431] [INFO] Task started: fastANI
[2024-01-24 13:19:59,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c5c718-3a9e-46fd-8f12-10192f12b615/GCF_008831155.1_ASM883115v1_genomic.fna.gz --refList GCF_008831155.1_ASM883115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008831155.1_ASM883115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:08,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:08,749] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:08,749] [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_008831155.1	s__Gulosibacter chungangensis	100.0	1068	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425685.1	s__Gulosibacter molinativorax	81.1392	502	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	99.97	99.97	0.98	0.98	2	-
GCF_900163695.1	s__Gulosibacter sp900163695	78.9906	340	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626105.1	s__Gulosibacter sp900626105	78.5694	249	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000381765.1	s__Gulosibacter faecalis	78.3499	263	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865375.1	s__Gulosibacter macacae	78.2357	239	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667575.1	s__Mycetocola lacteus	77.301	88	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	77.2995	101	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	77.1123	110	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107435.1	s__Herbiconiux ginsengi	77.1045	112	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	76.9376	111	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104705.1	s__Agrococcus carbonis	76.8763	118	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	76.8723	109	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317045.1	s__Leifsonia sp002105485	76.7922	110	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_003667565.1	s__Mycetocola tolaasinivorans	76.7619	75	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204755.1	s__Brachybacterium aquaticum	76.5371	64	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:08,751] [INFO] GTDB search result was written to GCF_008831155.1_ASM883115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:08,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:08,754] [INFO] DFAST_QC result json was written to GCF_008831155.1_ASM883115v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:08,754] [INFO] DFAST_QC completed!
[2024-01-24 13:20:08,754] [INFO] Total running time: 0h1m7s