[2024-01-24 12:06:49,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:49,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:49,840] [INFO] DQC Reference Directory: /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference
[2024-01-24 12:06:51,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,081] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,081] [INFO] Running command: gunzip -c /var/lib/cwl/stgebae5ba1-b355-4c5c-9b77-71f597f10580/GCF_015278355.1_ASM1527835v1_genomic.fna.gz | prodigal -d GCF_015278355.1_ASM1527835v1_genomic.fna/cds.fna -a GCF_015278355.1_ASM1527835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:05,095] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:05,095] [INFO] Task started: HMMsearch
[2024-01-24 12:07:05,095] [INFO] Running command: hmmsearch --tblout GCF_015278355.1_ASM1527835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/reference_markers.hmm GCF_015278355.1_ASM1527835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:05,391] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:05,393] [INFO] Found 6/6 markers.
[2024-01-24 12:07:05,437] [INFO] Query marker FASTA was written to GCF_015278355.1_ASM1527835v1_genomic.fna/markers.fasta
[2024-01-24 12:07:05,437] [INFO] Task started: Blastn
[2024-01-24 12:07:05,437] [INFO] Running command: blastn -query GCF_015278355.1_ASM1527835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/reference_markers.fasta -out GCF_015278355.1_ASM1527835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:06,609] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:06,613] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:06,613] [INFO] Target genome list was writen to GCF_015278355.1_ASM1527835v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:06,618] [INFO] Task started: fastANI
[2024-01-24 12:07:06,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgebae5ba1-b355-4c5c-9b77-71f597f10580/GCF_015278355.1_ASM1527835v1_genomic.fna.gz --refList GCF_015278355.1_ASM1527835v1_genomic.fna/target_genomes.txt --output GCF_015278355.1_ASM1527835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:17,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:17,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:17,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:17,037] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:17,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:17,038] [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
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	99.9851	1452	1477	95	conclusive
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	84.9915	1058	1477	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	84.7138	926	1477	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	84.5828	1027	1477	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	83.7112	948	1477	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	83.4838	842	1477	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.2614	886	1477	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	83.2267	919	1477	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.5362	754	1477	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	82.4246	801	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:17,039] [INFO] DFAST Taxonomy check result was written to GCF_015278355.1_ASM1527835v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:17,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:17,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:17,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/checkm_data
[2024-01-24 12:07:17,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:17,083] [INFO] Task started: CheckM
[2024-01-24 12:07:17,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015278355.1_ASM1527835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015278355.1_ASM1527835v1_genomic.fna/checkm_input GCF_015278355.1_ASM1527835v1_genomic.fna/checkm_result
[2024-01-24 12:08:29,661] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:29,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:29,681] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:29,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:29,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015278355.1_ASM1527835v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:29,683] [INFO] Task started: Blastn
[2024-01-24 12:08:29,683] [INFO] Running command: blastn -query GCF_015278355.1_ASM1527835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2317200-d011-4b05-aa8a-98f9b2f41b02/dqc_reference/reference_markers_gtdb.fasta -out GCF_015278355.1_ASM1527835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:31,594] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:31,598] [INFO] Selected 12 target genomes.
[2024-01-24 12:08:31,598] [INFO] Target genome list was writen to GCF_015278355.1_ASM1527835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:31,608] [INFO] Task started: fastANI
[2024-01-24 12:08:31,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgebae5ba1-b355-4c5c-9b77-71f597f10580/GCF_015278355.1_ASM1527835v1_genomic.fna.gz --refList GCF_015278355.1_ASM1527835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015278355.1_ASM1527835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:44,256] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:44,275] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:44,275] [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_015278355.1	s__Microbacterium yannicii_B	100.0	1475	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010634855.1	s__Microbacterium sp010634855	87.8363	1108	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_001422925.1	s__Microbacterium sp001422925	85.2521	1029	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	85.0949	1003	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	85.0112	1055	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	84.7575	922	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	84.686	922	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	84.6385	936	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	84.5827	1027	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000380605.1	s__Microbacterium sp000380605	83.9599	956	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	83.7153	947	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	83.2494	887	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:44,277] [INFO] GTDB search result was written to GCF_015278355.1_ASM1527835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:44,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:44,280] [INFO] DFAST_QC result json was written to GCF_015278355.1_ASM1527835v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:44,281] [INFO] DFAST_QC completed!
[2024-01-24 12:08:44,281] [INFO] Total running time: 0h1m54s