[2024-01-24 11:26:13,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:13,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:13,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference
[2024-01-24 11:26:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,523] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f2750c7-e5d2-41b4-a309-a8f913290c78/GCF_008017445.1_ASM801744v1_genomic.fna.gz | prodigal -d GCF_008017445.1_ASM801744v1_genomic.fna/cds.fna -a GCF_008017445.1_ASM801744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:23,816] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:23,816] [INFO] Task started: HMMsearch
[2024-01-24 11:26:23,816] [INFO] Running command: hmmsearch --tblout GCF_008017445.1_ASM801744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/reference_markers.hmm GCF_008017445.1_ASM801744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:24,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:24,123] [INFO] Found 6/6 markers.
[2024-01-24 11:26:24,149] [INFO] Query marker FASTA was written to GCF_008017445.1_ASM801744v1_genomic.fna/markers.fasta
[2024-01-24 11:26:24,150] [INFO] Task started: Blastn
[2024-01-24 11:26:24,150] [INFO] Running command: blastn -query GCF_008017445.1_ASM801744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/reference_markers.fasta -out GCF_008017445.1_ASM801744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:25,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:25,110] [INFO] Selected 23 target genomes.
[2024-01-24 11:26:25,111] [INFO] Target genome list was writen to GCF_008017445.1_ASM801744v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:25,129] [INFO] Task started: fastANI
[2024-01-24 11:26:25,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f2750c7-e5d2-41b4-a309-a8f913290c78/GCF_008017445.1_ASM801744v1_genomic.fna.gz --refList GCF_008017445.1_ASM801744v1_genomic.fna/target_genomes.txt --output GCF_008017445.1_ASM801744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:39,849] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:39,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:39,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:39,867] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:39,867] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:39,868] [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 mitrae	strain=M4-8	GCA_008017445.1	664640	664640	type	True	100.0	934	935	95	conclusive
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	78.4866	255	935	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	78.4732	255	935	95	below_threshold
Microbacterium keratanolyticum	strain=DSM 8606	GCA_016907255.1	67574	67574	type	True	78.3477	258	935	95	below_threshold
Microbacterium gorillae	strain=G3	GCA_000826185.2	1231063	1231063	type	True	78.2644	262	935	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	78.0773	237	935	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	77.9426	287	935	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	77.9303	241	935	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.8751	254	935	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	77.8295	278	935	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	77.7961	243	935	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	77.7722	222	935	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	77.7324	256	935	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	77.6499	205	935	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	77.6442	205	935	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	77.6367	234	935	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	77.6358	220	935	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	77.6215	221	935	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	77.6101	183	935	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.3136	158	935	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.0428	197	935	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	76.5298	81	935	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	75.7318	86	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:39,869] [INFO] DFAST Taxonomy check result was written to GCF_008017445.1_ASM801744v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:39,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:39,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:39,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/checkm_data
[2024-01-24 11:26:39,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:39,906] [INFO] Task started: CheckM
[2024-01-24 11:26:39,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008017445.1_ASM801744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008017445.1_ASM801744v1_genomic.fna/checkm_input GCF_008017445.1_ASM801744v1_genomic.fna/checkm_result
[2024-01-24 11:27:13,373] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:13,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:13,394] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:13,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:13,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008017445.1_ASM801744v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:13,396] [INFO] Task started: Blastn
[2024-01-24 11:27:13,396] [INFO] Running command: blastn -query GCF_008017445.1_ASM801744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafad46d5-e269-4b14-ab44-94f85c5cdfd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_008017445.1_ASM801744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,687] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:14,688] [INFO] Target genome list was writen to GCF_008017445.1_ASM801744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,726] [INFO] Task started: fastANI
[2024-01-24 11:27:14,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f2750c7-e5d2-41b4-a309-a8f913290c78/GCF_008017445.1_ASM801744v1_genomic.fna.gz --refList GCF_008017445.1_ASM801744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008017445.1_ASM801744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:25,919] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:25,938] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:25,938] [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_008017445.1	s__Microbacterium mitrae	100.0	934	935	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_019061125.1	s__Microbacterium sp019061125	82.5285	603	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387575.1	s__Microbacterium sp003387575	78.3558	251	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907255.1	s__Microbacterium keratanolyticum	78.3477	258	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826185.2	s__Microbacterium gorillae	78.2611	263	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	78.2349	265	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	78.231	257	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_000455825.1	s__Microbacterium maritypicum_A	78.1115	240	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.67	97.88	0.89	0.87	11	-
GCF_017831975.1	s__Microbacterium terrae	78.0603	267	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002979435.1	s__Microbacterium sp002979435	78.0474	246	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907295.1	s__Microbacterium dextranolyticum	78.0268	237	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426925.1	s__Microbacterium sp001426925	77.9446	231	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_014837165.1	s__Microbacterium sp014837165	77.8751	254	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282805.1	s__Microbacterium hominis_B	77.7987	272	935	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	77.6538	204	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900292075.1	s__Microbacterium timonense	77.6372	234	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	77.6328	179	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217495.1	s__Microterricola gilva	77.6101	183	935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744855.1	s__Microbacterium sp017744855	77.3181	196	935	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 11:27:25,941] [INFO] GTDB search result was written to GCF_008017445.1_ASM801744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:25,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:25,947] [INFO] DFAST_QC result json was written to GCF_008017445.1_ASM801744v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:25,947] [INFO] DFAST_QC completed!
[2024-01-24 11:27:25,947] [INFO] Total running time: 0h1m13s