[2024-01-24 13:40:54,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:54,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:54,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference
[2024-01-24 13:40:56,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,255] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgf70cfc4f-5dd8-4cad-8fd9-e4c734975081/GCF_027921965.1_ASM2792196v1_genomic.fna.gz | prodigal -d GCF_027921965.1_ASM2792196v1_genomic.fna/cds.fna -a GCF_027921965.1_ASM2792196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:06,189] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:06,190] [INFO] Task started: HMMsearch
[2024-01-24 13:41:06,190] [INFO] Running command: hmmsearch --tblout GCF_027921965.1_ASM2792196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/reference_markers.hmm GCF_027921965.1_ASM2792196v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,463] [INFO] Found 6/6 markers.
[2024-01-24 13:41:06,496] [INFO] Query marker FASTA was written to GCF_027921965.1_ASM2792196v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,497] [INFO] Task started: Blastn
[2024-01-24 13:41:06,497] [INFO] Running command: blastn -query GCF_027921965.1_ASM2792196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/reference_markers.fasta -out GCF_027921965.1_ASM2792196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,660] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,664] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:07,665] [INFO] Target genome list was writen to GCF_027921965.1_ASM2792196v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:07,684] [INFO] Task started: fastANI
[2024-01-24 13:41:07,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgf70cfc4f-5dd8-4cad-8fd9-e4c734975081/GCF_027921965.1_ASM2792196v1_genomic.fna.gz --refList GCF_027921965.1_ASM2792196v1_genomic.fna/target_genomes.txt --output GCF_027921965.1_ASM2792196v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:24,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:24,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:24,651] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:24,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:24,651] [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	99.9977	1019	1019	95	conclusive
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.9444	486	1019	95	below_threshold
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	80.8577	547	1019	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.7857	514	1019	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	80.7127	489	1019	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	80.6214	533	1019	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	80.6149	550	1019	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	80.4143	531	1019	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.4028	517	1019	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	80.371	534	1019	95	below_threshold
Microbacterium saperdae	strain=DSM 20169	GCA_006716345.1	69368	69368	type	True	80.3644	549	1019	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	80.3437	550	1019	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	80.3368	526	1019	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	80.3156	521	1019	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	80.2803	534	1019	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	80.2633	472	1019	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	80.218	478	1019	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.6288	425	1019	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.5527	382	1019	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	79.5401	426	1019	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	79.5204	401	1019	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.4909	434	1019	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.2678	379	1019	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.203	401	1019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,655] [INFO] DFAST Taxonomy check result was written to GCF_027921965.1_ASM2792196v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:24,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:24,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:24,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/checkm_data
[2024-01-24 13:41:24,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:24,698] [INFO] Task started: CheckM
[2024-01-24 13:41:24,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921965.1_ASM2792196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921965.1_ASM2792196v1_genomic.fna/checkm_input GCF_027921965.1_ASM2792196v1_genomic.fna/checkm_result
[2024-01-24 13:42:16,453] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:16,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,472] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:16,472] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:16,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921965.1_ASM2792196v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:16,473] [INFO] Task started: Blastn
[2024-01-24 13:42:16,473] [INFO] Running command: blastn -query GCF_027921965.1_ASM2792196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ee08de-3887-488c-9f7e-06f911971cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921965.1_ASM2792196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:18,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:18,110] [INFO] Selected 25 target genomes.
[2024-01-24 13:42:18,110] [INFO] Target genome list was writen to GCF_027921965.1_ASM2792196v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:18,128] [INFO] Task started: fastANI
[2024-01-24 13:42:18,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgf70cfc4f-5dd8-4cad-8fd9-e4c734975081/GCF_027921965.1_ASM2792196v1_genomic.fna.gz --refList GCF_027921965.1_ASM2792196v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921965.1_ASM2792196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:35,368] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:35,392] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:35,392] [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	99.9977	1019	1019	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	81.0696	420	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075395.1	s__Microbacterium sp003075395	80.8272	560	1019	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	80.8203	538	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	98.29	96.93	0.91	0.85	10	-
GCF_001049495.1	s__Microbacterium sp001049495	80.7776	513	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939615.1	s__Microbacterium sp017939615	80.7669	507	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794315.1	s__Microbacterium sp004794315	80.7283	533	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.84	0.93	0.91	3	-
GCA_008868125.1	s__Microbacterium maritypicum	80.7256	549	1019	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	80.7184	550	1019	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	80.6708	525	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	-
GCF_000967865.1	s__Microbacterium sp000967865	80.61	519	1019	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	80.6088	550	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002257455.1	s__Microbacterium sp002257455	80.5017	463	1019	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	80.3925	506	1019	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	80.3783	530	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
GCF_002872075.1	s__Microbacterium kitamiense	80.3769	547	1019	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	80.3308	510	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_003610275.1	s__Microbacterium ginsengiterrae_A	80.2987	520	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306305.1	s__Microbacterium sp017306305	80.2925	531	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCA_017744855.1	s__Microbacterium sp017744855	80.2868	417	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	80.27	516	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_018268435.1	s__Microbacterium sp018268435	80.0677	462	1019	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268515.1	s__Microbacterium sp018268515	80.0529	473	1019	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	80.0409	467	1019	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	79.2078	407	1019	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 13:42:35,394] [INFO] GTDB search result was written to GCF_027921965.1_ASM2792196v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:35,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:35,400] [INFO] DFAST_QC result json was written to GCF_027921965.1_ASM2792196v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:35,400] [INFO] DFAST_QC completed!
[2024-01-24 13:42:35,400] [INFO] Total running time: 0h1m41s