[2024-01-24 12:31:21,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference
[2024-01-24 12:31:22,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,723] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc46e9c5-69ac-4da5-bc40-2af3230134d8/GCF_006539145.1_ASM653914v1_genomic.fna.gz | prodigal -d GCF_006539145.1_ASM653914v1_genomic.fna/cds.fna -a GCF_006539145.1_ASM653914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:33,216] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:33,217] [INFO] Task started: HMMsearch
[2024-01-24 12:31:33,217] [INFO] Running command: hmmsearch --tblout GCF_006539145.1_ASM653914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/reference_markers.hmm GCF_006539145.1_ASM653914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:33,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:33,426] [INFO] Found 6/6 markers.
[2024-01-24 12:31:33,460] [INFO] Query marker FASTA was written to GCF_006539145.1_ASM653914v1_genomic.fna/markers.fasta
[2024-01-24 12:31:33,461] [INFO] Task started: Blastn
[2024-01-24 12:31:33,461] [INFO] Running command: blastn -query GCF_006539145.1_ASM653914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/reference_markers.fasta -out GCF_006539145.1_ASM653914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:34,556] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:34,558] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:34,559] [INFO] Target genome list was writen to GCF_006539145.1_ASM653914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:34,564] [INFO] Task started: fastANI
[2024-01-24 12:31:34,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc46e9c5-69ac-4da5-bc40-2af3230134d8/GCF_006539145.1_ASM653914v1_genomic.fna.gz --refList GCF_006539145.1_ASM653914v1_genomic.fna/target_genomes.txt --output GCF_006539145.1_ASM653914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:44,511] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:44,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:44,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:44,522] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:44,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:44,522] [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 testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	100.0	1180	1181	95	conclusive
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	85.4588	840	1181	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	85.4334	842	1181	95	below_threshold
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	84.9986	811	1181	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.4691	529	1181	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	80.3654	515	1181	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.3459	510	1181	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	80.2726	485	1181	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.2565	520	1181	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.2052	534	1181	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.2003	519	1181	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.087	521	1181	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.9197	527	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:44,523] [INFO] DFAST Taxonomy check result was written to GCF_006539145.1_ASM653914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:44,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:44,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:44,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/checkm_data
[2024-01-24 12:31:44,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:44,560] [INFO] Task started: CheckM
[2024-01-24 12:31:44,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539145.1_ASM653914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539145.1_ASM653914v1_genomic.fna/checkm_input GCF_006539145.1_ASM653914v1_genomic.fna/checkm_result
[2024-01-24 12:32:31,883] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:31,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:31,905] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:31,905] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:31,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539145.1_ASM653914v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:31,906] [INFO] Task started: Blastn
[2024-01-24 12:32:31,906] [INFO] Running command: blastn -query GCF_006539145.1_ASM653914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8074d44d-148a-46e7-85a5-167180461f1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539145.1_ASM653914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:33,533] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:33,537] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:33,538] [INFO] Target genome list was writen to GCF_006539145.1_ASM653914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:33,562] [INFO] Task started: fastANI
[2024-01-24 12:32:33,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc46e9c5-69ac-4da5-bc40-2af3230134d8/GCF_006539145.1_ASM653914v1_genomic.fna.gz --refList GCF_006539145.1_ASM653914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539145.1_ASM653914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:39,795] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:39,802] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:39,803] [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_006539145.1	s__Microbacterium testaceum	100.0	1180	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.70	98.67	0.94	0.93	3	conclusive
GCF_017833635.1	s__Microbacterium sp017833635	91.066	974	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386675.1	s__Microbacterium chocolatum_A	90.9381	995	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.92	0.92	2	-
GCF_900104345.1	s__Microbacterium testaceum_A	88.8767	979	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.34	95.96	0.91	0.90	3	-
GCF_008763945.1	s__Microbacterium testaceum_G	88.5588	922	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679045.1	s__Microbacterium sp007679045	86.401	868	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_003075375.1	s__Microbacterium testaceum_E	85.6823	813	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,805] [INFO] GTDB search result was written to GCF_006539145.1_ASM653914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:39,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:39,810] [INFO] DFAST_QC result json was written to GCF_006539145.1_ASM653914v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:39,810] [INFO] DFAST_QC completed!
[2024-01-24 12:32:39,810] [INFO] Total running time: 0h1m19s