[2024-01-25 19:47:35,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference
[2024-01-25 19:47:36,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,831] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdf89dd0-a6cb-4c35-b87f-b1e08302e1f4/GCF_008868005.1_ASM886800v1_genomic.fna.gz | prodigal -d GCF_008868005.1_ASM886800v1_genomic.fna/cds.fna -a GCF_008868005.1_ASM886800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:45,998] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:45,998] [INFO] Task started: HMMsearch
[2024-01-25 19:47:45,998] [INFO] Running command: hmmsearch --tblout GCF_008868005.1_ASM886800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/reference_markers.hmm GCF_008868005.1_ASM886800v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:46,243] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:46,244] [INFO] Found 6/6 markers.
[2024-01-25 19:47:46,276] [INFO] Query marker FASTA was written to GCF_008868005.1_ASM886800v1_genomic.fna/markers.fasta
[2024-01-25 19:47:46,276] [INFO] Task started: Blastn
[2024-01-25 19:47:46,277] [INFO] Running command: blastn -query GCF_008868005.1_ASM886800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/reference_markers.fasta -out GCF_008868005.1_ASM886800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:47,384] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:47,388] [INFO] Selected 14 target genomes.
[2024-01-25 19:47:47,389] [INFO] Target genome list was writen to GCF_008868005.1_ASM886800v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:47,397] [INFO] Task started: fastANI
[2024-01-25 19:47:47,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf89dd0-a6cb-4c35-b87f-b1e08302e1f4/GCF_008868005.1_ASM886800v1_genomic.fna.gz --refList GCF_008868005.1_ASM886800v1_genomic.fna/target_genomes.txt --output GCF_008868005.1_ASM886800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:58,268] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:58,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:58,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:58,278] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:58,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:58,278] [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 algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	100.0	1208	1208	95	conclusive
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	85.7641	913	1208	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	85.7238	919	1208	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	85.659	814	1208	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	85.6264	806	1208	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	85.2588	786	1208	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	85.0835	890	1208	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	83.3964	812	1208	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	83.3076	786	1208	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.5117	570	1208	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.3988	601	1208	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.8285	451	1208	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.6175	515	1208	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.513	491	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:58,281] [INFO] DFAST Taxonomy check result was written to GCF_008868005.1_ASM886800v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:58,282] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:58,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:58,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/checkm_data
[2024-01-25 19:47:58,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:58,322] [INFO] Task started: CheckM
[2024-01-25 19:47:58,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008868005.1_ASM886800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008868005.1_ASM886800v1_genomic.fna/checkm_input GCF_008868005.1_ASM886800v1_genomic.fna/checkm_result
[2024-01-25 19:48:56,317] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:56,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:56,336] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:56,336] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:56,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008868005.1_ASM886800v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:56,337] [INFO] Task started: Blastn
[2024-01-25 19:48:56,337] [INFO] Running command: blastn -query GCF_008868005.1_ASM886800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac371695-7291-43ab-a18c-3a1ba2675abc/dqc_reference/reference_markers_gtdb.fasta -out GCF_008868005.1_ASM886800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:58,193] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:58,196] [INFO] Selected 16 target genomes.
[2024-01-25 19:48:58,196] [INFO] Target genome list was writen to GCF_008868005.1_ASM886800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:58,215] [INFO] Task started: fastANI
[2024-01-25 19:48:58,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf89dd0-a6cb-4c35-b87f-b1e08302e1f4/GCF_008868005.1_ASM886800v1_genomic.fna.gz --refList GCF_008868005.1_ASM886800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008868005.1_ASM886800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:12,403] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:12,413] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:12,413] [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_008868005.1	s__Microbacterium algeriense	100.0	1208	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.81	98.72	0.94	0.93	3	conclusive
GCF_002979435.1	s__Microbacterium sp002979435	85.7201	868	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540085.1	s__Microbacterium oxydans	85.7189	919	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.85	98.27	0.91	0.87	12	-
GCA_008868125.1	s__Microbacterium maritypicum	85.7028	891	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_002979475.1	s__Microbacterium sp002979475	85.6758	889	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794515.1	s__Microbacterium sp004794515	85.6451	904	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014171575.1	s__Microbacterium sp014171575	85.5752	913	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979655.1	s__Microbacterium sp002979655	85.5731	877	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_000455825.1	s__Microbacterium maritypicum_A	85.4683	871	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.67	97.88	0.89	0.87	11	-
GCF_900095745.1	s__Microbacterium oxydans_B	85.4375	876	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.33	97.96	0.92	0.90	3	-
GCF_000956405.1	s__Microbacterium oxydans_C	85.378	849	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019056515.1	s__Microbacterium sp001595495	85.0996	897	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	98.29	96.93	0.91	0.85	10	-
GCF_004794315.1	s__Microbacterium sp004794315	84.891	857	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.84	0.93	0.91	3	-
GCF_003075395.1	s__Microbacterium sp003075395	84.1627	866	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967865.1	s__Microbacterium sp000967865	83.6451	805	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405925.1	s__Microbacterium sp017405925	83.4078	585	1208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:12,415] [INFO] GTDB search result was written to GCF_008868005.1_ASM886800v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:12,415] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:12,418] [INFO] DFAST_QC result json was written to GCF_008868005.1_ASM886800v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:12,418] [INFO] DFAST_QC completed!
[2024-01-25 19:49:12,418] [INFO] Total running time: 0h1m37s