[2024-01-24 10:48:09,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,558] [INFO] DQC Reference Directory: /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,958] [INFO] Running command: gunzip -c /var/lib/cwl/stga28af5b3-1b37-45d0-971f-a99a7c9fc493/GCF_003148845.1_ASM314884v1_genomic.fna.gz | prodigal -d GCF_003148845.1_ASM314884v1_genomic.fna/cds.fna -a GCF_003148845.1_ASM314884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:49,150] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:49,151] [INFO] Task started: HMMsearch
[2024-01-24 10:48:49,151] [INFO] Running command: hmmsearch --tblout GCF_003148845.1_ASM314884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/reference_markers.hmm GCF_003148845.1_ASM314884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:49,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:49,511] [INFO] Found 6/6 markers.
[2024-01-24 10:48:49,562] [INFO] Query marker FASTA was written to GCF_003148845.1_ASM314884v1_genomic.fna/markers.fasta
[2024-01-24 10:48:49,563] [INFO] Task started: Blastn
[2024-01-24 10:48:49,563] [INFO] Running command: blastn -query GCF_003148845.1_ASM314884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/reference_markers.fasta -out GCF_003148845.1_ASM314884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:50,183] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:50,187] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:50,187] [INFO] Target genome list was writen to GCF_003148845.1_ASM314884v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:50,193] [INFO] Task started: fastANI
[2024-01-24 10:48:50,193] [INFO] Running command: fastANI --query /var/lib/cwl/stga28af5b3-1b37-45d0-971f-a99a7c9fc493/GCF_003148845.1_ASM314884v1_genomic.fna.gz --refList GCF_003148845.1_ASM314884v1_genomic.fna/target_genomes.txt --output GCF_003148845.1_ASM314884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:11,035] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:11,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:11,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:11,051] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:11,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:11,052] [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
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	100.0	1956	1957	95	conclusive
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	84.2513	1371	1957	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	81.1432	1056	1957	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	81.0753	1044	1957	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	81.0733	1108	1957	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	80.9762	1087	1957	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	80.9717	1081	1957	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	78.3725	636	1957	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.9147	389	1957	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.7957	370	1957	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.7823	282	1957	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.6565	307	1957	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.4928	383	1957	95	below_threshold
Mucilaginibacter paludis	strain=DSM 18603	GCA_000166195.3	423351	423351	type	True	77.1249	309	1957	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	76.2849	55	1957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:11,053] [INFO] DFAST Taxonomy check result was written to GCF_003148845.1_ASM314884v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:11,054] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:11,054] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:11,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/checkm_data
[2024-01-24 10:49:11,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:11,131] [INFO] Task started: CheckM
[2024-01-24 10:49:11,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148845.1_ASM314884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148845.1_ASM314884v1_genomic.fna/checkm_input GCF_003148845.1_ASM314884v1_genomic.fna/checkm_result
[2024-01-24 10:50:23,397] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:23,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:23,437] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:23,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:23,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148845.1_ASM314884v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:23,438] [INFO] Task started: Blastn
[2024-01-24 10:50:23,439] [INFO] Running command: blastn -query GCF_003148845.1_ASM314884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5541db5-9dfc-4fd4-9719-56a8d9a29203/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148845.1_ASM314884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:24,245] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:24,249] [INFO] Selected 12 target genomes.
[2024-01-24 10:50:24,249] [INFO] Target genome list was writen to GCF_003148845.1_ASM314884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:24,258] [INFO] Task started: fastANI
[2024-01-24 10:50:24,258] [INFO] Running command: fastANI --query /var/lib/cwl/stga28af5b3-1b37-45d0-971f-a99a7c9fc493/GCF_003148845.1_ASM314884v1_genomic.fna.gz --refList GCF_003148845.1_ASM314884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148845.1_ASM314884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:42,110] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:42,125] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:42,125] [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_003148845.1	s__Mucilaginibacter oryzae	100.0	1956	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003576455.2	s__Mucilaginibacter celer	84.2677	1367	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643835.1	s__Mucilaginibacter rubeus	81.1331	1058	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_003351025.1	s__Mucilaginibacter endophyticus	81.0757	1109	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	81.06	1047	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	80.9917	1111	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	80.9819	1079	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675385.1	s__Mucilaginibacter kameinonensis	80.9733	1088	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	80.8992	1075	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846085.1	s__Mucilaginibacter sp007846085	77.7712	283	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166195.2	s__Mucilaginibacter paludis	77.1207	312	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266935.1	s__Mucilaginibacter sp018266935	76.7038	162	1957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:42,127] [INFO] GTDB search result was written to GCF_003148845.1_ASM314884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:42,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:42,131] [INFO] DFAST_QC result json was written to GCF_003148845.1_ASM314884v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:42,132] [INFO] DFAST_QC completed!
[2024-01-24 10:50:42,132] [INFO] Total running time: 0h2m33s