[2024-01-24 12:31:34,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference
[2024-01-24 12:31:35,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,601] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,601] [INFO] Running command: gunzip -c /var/lib/cwl/stgae1f0774-8b50-469b-ac1f-08a0c2cd42ad/GCF_007362775.1_ASM736277v1_genomic.fna.gz | prodigal -d GCF_007362775.1_ASM736277v1_genomic.fna/cds.fna -a GCF_007362775.1_ASM736277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:51,025] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:51,026] [INFO] Task started: HMMsearch
[2024-01-24 12:31:51,026] [INFO] Running command: hmmsearch --tblout GCF_007362775.1_ASM736277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/reference_markers.hmm GCF_007362775.1_ASM736277v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:51,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:51,400] [INFO] Found 6/6 markers.
[2024-01-24 12:31:51,447] [INFO] Query marker FASTA was written to GCF_007362775.1_ASM736277v1_genomic.fna/markers.fasta
[2024-01-24 12:31:51,447] [INFO] Task started: Blastn
[2024-01-24 12:31:51,448] [INFO] Running command: blastn -query GCF_007362775.1_ASM736277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/reference_markers.fasta -out GCF_007362775.1_ASM736277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:52,572] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:52,576] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:52,576] [INFO] Target genome list was writen to GCF_007362775.1_ASM736277v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:52,607] [INFO] Task started: fastANI
[2024-01-24 12:31:52,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1f0774-8b50-469b-ac1f-08a0c2cd42ad/GCF_007362775.1_ASM736277v1_genomic.fna.gz --refList GCF_007362775.1_ASM736277v1_genomic.fna/target_genomes.txt --output GCF_007362775.1_ASM736277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:04,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:04,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:04,661] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:04,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:04,662] [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
Microlunatus elymi	strain=KUDC0627	GCA_007362775.1	2596828	2596828	type	True	100.0	1707	1707	95	conclusive
Microlunatus soli	strain=DSM 21800	GCA_900105385.1	630515	630515	type	True	81.0357	960	1707	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	80.0263	790	1707	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	78.764	566	1707	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.4682	642	1707	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	78.3096	443	1707	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.732	403	1707	95	below_threshold
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	77.6964	279	1707	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.6784	366	1707	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	77.6524	272	1707	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.2753	251	1707	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.1874	187	1707	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.1087	261	1707	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	76.8375	238	1707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,663] [INFO] DFAST Taxonomy check result was written to GCF_007362775.1_ASM736277v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:04,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:04,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:04,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/checkm_data
[2024-01-24 12:32:04,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:04,719] [INFO] Task started: CheckM
[2024-01-24 12:32:04,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007362775.1_ASM736277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007362775.1_ASM736277v1_genomic.fna/checkm_input GCF_007362775.1_ASM736277v1_genomic.fna/checkm_result
[2024-01-24 12:33:10,112] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:10,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:10,135] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:10,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:10,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007362775.1_ASM736277v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:10,136] [INFO] Task started: Blastn
[2024-01-24 12:33:10,136] [INFO] Running command: blastn -query GCF_007362775.1_ASM736277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec4bf64-31e0-4cab-91db-dd0d15fd11da/dqc_reference/reference_markers_gtdb.fasta -out GCF_007362775.1_ASM736277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:11,742] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:11,746] [INFO] Selected 11 target genomes.
[2024-01-24 12:33:11,747] [INFO] Target genome list was writen to GCF_007362775.1_ASM736277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:11,755] [INFO] Task started: fastANI
[2024-01-24 12:33:11,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1f0774-8b50-469b-ac1f-08a0c2cd42ad/GCF_007362775.1_ASM736277v1_genomic.fna.gz --refList GCF_007362775.1_ASM736277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007362775.1_ASM736277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:23,017] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:23,037] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:23,037] [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_007362775.1	s__Microlunatus_A sp007362775	100.0	1707	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408315.1	s__Microlunatus_A terrae	81.7919	942	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105385.1	s__Microlunatus_A soli	81.0747	954	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646195.1	s__Microlunatus_A endophyticus	80.0547	785	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707365.1	s__Microlunatus_A sp009707365	79.8689	778	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	78.787	563	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407955.1	s__Microlunatus_B parietis	78.4685	641	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907535.1	s__Microlunatus_C panaciterrae	78.3103	443	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	78.1173	460	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193425.1	s__Friedmanniella antarctica	77.6675	364	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	77.0109	278	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:23,039] [INFO] GTDB search result was written to GCF_007362775.1_ASM736277v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:23,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:23,048] [INFO] DFAST_QC result json was written to GCF_007362775.1_ASM736277v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:23,048] [INFO] DFAST_QC completed!
[2024-01-24 12:33:23,048] [INFO] Total running time: 0h1m49s