[2024-01-25 17:53:20,543] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:20,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:20,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference
[2024-01-25 17:53:21,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:21,720] [INFO] Task started: Prodigal
[2024-01-25 17:53:21,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f834c90-e709-424e-a86e-31271d93e6d5/GCF_016907255.1_ASM1690725v1_genomic.fna.gz | prodigal -d GCF_016907255.1_ASM1690725v1_genomic.fna/cds.fna -a GCF_016907255.1_ASM1690725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:30,042] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:30,042] [INFO] Task started: HMMsearch
[2024-01-25 17:53:30,042] [INFO] Running command: hmmsearch --tblout GCF_016907255.1_ASM1690725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/reference_markers.hmm GCF_016907255.1_ASM1690725v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:30,253] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:30,254] [INFO] Found 6/6 markers.
[2024-01-25 17:53:30,279] [INFO] Query marker FASTA was written to GCF_016907255.1_ASM1690725v1_genomic.fna/markers.fasta
[2024-01-25 17:53:30,279] [INFO] Task started: Blastn
[2024-01-25 17:53:30,279] [INFO] Running command: blastn -query GCF_016907255.1_ASM1690725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/reference_markers.fasta -out GCF_016907255.1_ASM1690725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:31,264] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:31,267] [INFO] Selected 24 target genomes.
[2024-01-25 17:53:31,267] [INFO] Target genome list was writen to GCF_016907255.1_ASM1690725v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:31,294] [INFO] Task started: fastANI
[2024-01-25 17:53:31,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f834c90-e709-424e-a86e-31271d93e6d5/GCF_016907255.1_ASM1690725v1_genomic.fna.gz --refList GCF_016907255.1_ASM1690725v1_genomic.fna/target_genomes.txt --output GCF_016907255.1_ASM1690725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:46,597] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:46,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:46,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:46,611] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:46,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:46,612] [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 keratanolyticum	strain=DSM 8606	GCA_016907255.1	67574	67574	type	True	100.0	1021	1022	95	conclusive
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.9733	484	1022	95	below_threshold
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	80.8628	545	1022	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	80.7928	479	1022	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	80.7894	521	1022	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	80.7486	536	1022	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.7109	516	1022	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	80.6576	515	1022	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	80.652	517	1022	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	80.6516	520	1022	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	80.5695	519	1022	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	80.5503	541	1022	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.5425	510	1022	95	below_threshold
Microbacterium saperdae	strain=DSM 20169	GCA_006716345.1	69368	69368	type	True	80.5062	545	1022	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	80.3905	548	1022	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	80.2414	459	1022	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	80.2031	468	1022	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.6854	431	1022	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.5535	425	1022	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.5366	388	1022	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	79.5299	418	1022	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	79.503	388	1022	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.4711	380	1022	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.3519	403	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:46,613] [INFO] DFAST Taxonomy check result was written to GCF_016907255.1_ASM1690725v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:46,613] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:46,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:46,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/checkm_data
[2024-01-25 17:53:46,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:46,646] [INFO] Task started: CheckM
[2024-01-25 17:53:46,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907255.1_ASM1690725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907255.1_ASM1690725v1_genomic.fna/checkm_input GCF_016907255.1_ASM1690725v1_genomic.fna/checkm_result
[2024-01-25 17:54:33,387] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:33,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:33,411] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:33,411] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:33,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907255.1_ASM1690725v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:33,412] [INFO] Task started: Blastn
[2024-01-25 17:54:33,412] [INFO] Running command: blastn -query GCF_016907255.1_ASM1690725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76903b8-d765-4298-ba82-dfe0adfd3402/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907255.1_ASM1690725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:35,091] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:35,093] [INFO] Selected 25 target genomes.
[2024-01-25 17:54:35,094] [INFO] Target genome list was writen to GCF_016907255.1_ASM1690725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:35,160] [INFO] Task started: fastANI
[2024-01-25 17:54:35,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f834c90-e709-424e-a86e-31271d93e6d5/GCF_016907255.1_ASM1690725v1_genomic.fna.gz --refList GCF_016907255.1_ASM1690725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907255.1_ASM1690725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:53,998] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:54,012] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:54,013] [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_016907255.1	s__Microbacterium keratanolyticum	100.0	1022	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017405925.1	s__Microbacterium sp017405925	81.2918	415	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866135.1	s__Microbacterium sp001866135	80.8509	524	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	-
GCF_003075395.1	s__Microbacterium sp003075395	80.8373	575	1022	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	80.8206	545	1022	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	80.8202	542	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.84	0.93	0.91	3	-
GCF_001049495.1	s__Microbacterium sp001049495	80.7617	515	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008868125.1	s__Microbacterium maritypicum	80.7319	549	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_000956525.1	s__Microbacterium oxydans_A	80.7019	552	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904066215.1	s__Microbacterium sp002456035	80.6479	527	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
GCF_004794515.1	s__Microbacterium sp004794515	80.6253	553	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017306305.1	s__Microbacterium sp017306305	80.5676	518	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCF_017939615.1	s__Microbacterium sp017939615	80.5501	541	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610275.1	s__Microbacterium ginsengiterrae_A	80.5485	508	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257455.1	s__Microbacterium sp002257455	80.5372	458	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513675.1	s__Microbacterium sp001513675	80.5287	513	1022	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	80.5255	522	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872075.1	s__Microbacterium kitamiense	80.5123	538	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956545.1	s__Microbacterium azadirachtae	80.4558	507	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	80.3806	517	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_018268515.1	s__Microbacterium sp018268515	80.296	466	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268435.1	s__Microbacterium sp018268435	80.2504	449	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744855.1	s__Microbacterium sp017744855	80.1944	432	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268455.1	s__Microbacterium sp018268455	80.1898	463	1022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155915.1	s__Microbacterium sp900155915	79.6595	392	1022	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 17:54:54,018] [INFO] GTDB search result was written to GCF_016907255.1_ASM1690725v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:54,018] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:54,028] [INFO] DFAST_QC result json was written to GCF_016907255.1_ASM1690725v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:54,028] [INFO] DFAST_QC completed!
[2024-01-25 17:54:54,028] [INFO] Total running time: 0h1m33s