[2024-01-25 19:07:50,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:50,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:50,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference
[2024-01-25 19:07:51,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:51,712] [INFO] Task started: Prodigal
[2024-01-25 19:07:51,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgaff3a163-414a-4f73-ad30-d00dbcb8a959/GCF_024971095.1_ASM2497109v1_genomic.fna.gz | prodigal -d GCF_024971095.1_ASM2497109v1_genomic.fna/cds.fna -a GCF_024971095.1_ASM2497109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:58,196] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:58,197] [INFO] Task started: HMMsearch
[2024-01-25 19:07:58,197] [INFO] Running command: hmmsearch --tblout GCF_024971095.1_ASM2497109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/reference_markers.hmm GCF_024971095.1_ASM2497109v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:58,399] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:58,400] [INFO] Found 6/6 markers.
[2024-01-25 19:07:58,421] [INFO] Query marker FASTA was written to GCF_024971095.1_ASM2497109v1_genomic.fna/markers.fasta
[2024-01-25 19:07:58,421] [INFO] Task started: Blastn
[2024-01-25 19:07:58,421] [INFO] Running command: blastn -query GCF_024971095.1_ASM2497109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/reference_markers.fasta -out GCF_024971095.1_ASM2497109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:59,725] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:59,727] [INFO] Selected 19 target genomes.
[2024-01-25 19:07:59,727] [INFO] Target genome list was writen to GCF_024971095.1_ASM2497109v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:59,751] [INFO] Task started: fastANI
[2024-01-25 19:07:59,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff3a163-414a-4f73-ad30-d00dbcb8a959/GCF_024971095.1_ASM2497109v1_genomic.fna.gz --refList GCF_024971095.1_ASM2497109v1_genomic.fna/target_genomes.txt --output GCF_024971095.1_ASM2497109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:12,783] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:12,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:12,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:12,799] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:08:12,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:08:12,799] [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 bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	82.6854	577	848	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	82.5146	581	848	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	82.2107	593	848	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	82.0696	503	848	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	82.0589	563	848	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	81.8698	534	848	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	81.7961	530	848	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	81.6195	502	848	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	81.4601	567	848	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	81.4092	556	848	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	81.0276	528	848	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	80.9009	531	848	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.635	487	848	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.5147	425	848	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	80.4842	459	848	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.4494	472	848	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	80.1412	404	848	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	78.6512	290	848	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	78.462	285	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:12,805] [INFO] DFAST Taxonomy check result was written to GCF_024971095.1_ASM2497109v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:12,805] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:12,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:12,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/checkm_data
[2024-01-25 19:08:12,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:12,860] [INFO] Task started: CheckM
[2024-01-25 19:08:12,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024971095.1_ASM2497109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024971095.1_ASM2497109v1_genomic.fna/checkm_input GCF_024971095.1_ASM2497109v1_genomic.fna/checkm_result
[2024-01-25 19:08:56,959] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:56,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:56,979] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:56,979] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:56,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024971095.1_ASM2497109v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:56,980] [INFO] Task started: Blastn
[2024-01-25 19:08:56,980] [INFO] Running command: blastn -query GCF_024971095.1_ASM2497109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094f833c-5fa9-458b-9a74-9f60a21d82ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_024971095.1_ASM2497109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:59,380] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:59,383] [INFO] Selected 22 target genomes.
[2024-01-25 19:08:59,383] [INFO] Target genome list was writen to GCF_024971095.1_ASM2497109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:59,445] [INFO] Task started: fastANI
[2024-01-25 19:08:59,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff3a163-414a-4f73-ad30-d00dbcb8a959/GCF_024971095.1_ASM2497109v1_genomic.fna.gz --refList GCF_024971095.1_ASM2497109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024971095.1_ASM2497109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:15,397] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:15,410] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:09:15,411] [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_015040615.1	s__Microbacterium sp015040615	83.5608	618	848	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	82.8469	572	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCA_001897945.1	s__Microbacterium sp001897945	82.8303	596	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	82.7131	584	848	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	82.7096	575	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752045.1	s__Microbacterium sp001639925	82.6844	607	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.61	99.21	0.98	0.97	3	-
GCF_001878835.1	s__Microbacterium sp001878835	82.6245	546	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.56	98.56	0.87	0.87	2	-
GCF_014084045.1	s__Microbacterium esteraromaticum_D	82.4987	593	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002837415.1	s__Microbacterium sp002837415	82.4663	553	848	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	82.2143	462	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105335.1	s__Microbacterium paraoxydans	82.0501	564	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
GCF_902506375.1	s__Microbacterium sp902506375	82.0329	565	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408055.1	s__Microbacterium esteraromaticum_C	81.9117	547	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.47	97.77	0.93	0.90	5	-
GCF_001866135.1	s__Microbacterium sp001866135	81.8412	560	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	-
GCF_000956545.1	s__Microbacterium azadirachtae	81.8274	537	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_001552355.1	s__Microbacterium resistens	81.8105	530	848	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	81.6928	559	848	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	81.6919	566	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCF_013409745.1	s__Microbacterium pseudoresistens	81.6323	499	848	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	81.6249	525	848	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	81.4889	459	848	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	81.3564	553	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:15,412] [INFO] GTDB search result was written to GCF_024971095.1_ASM2497109v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:15,413] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:15,417] [INFO] DFAST_QC result json was written to GCF_024971095.1_ASM2497109v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:15,417] [INFO] DFAST_QC completed!
[2024-01-25 19:09:15,418] [INFO] Total running time: 0h1m25s