[2024-01-25 17:42:35,348] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:35,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:35,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference
[2024-01-25 17:42:36,491] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:36,492] [INFO] Task started: Prodigal
[2024-01-25 17:42:36,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e109ec9-49af-4b69-9455-29b4449e8c01/GCF_015278285.1_ASM1527828v1_genomic.fna.gz | prodigal -d GCF_015278285.1_ASM1527828v1_genomic.fna/cds.fna -a GCF_015278285.1_ASM1527828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:45,978] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:45,978] [INFO] Task started: HMMsearch
[2024-01-25 17:42:45,978] [INFO] Running command: hmmsearch --tblout GCF_015278285.1_ASM1527828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/reference_markers.hmm GCF_015278285.1_ASM1527828v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:46,177] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:46,178] [INFO] Found 6/6 markers.
[2024-01-25 17:42:46,206] [INFO] Query marker FASTA was written to GCF_015278285.1_ASM1527828v1_genomic.fna/markers.fasta
[2024-01-25 17:42:46,206] [INFO] Task started: Blastn
[2024-01-25 17:42:46,206] [INFO] Running command: blastn -query GCF_015278285.1_ASM1527828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/reference_markers.fasta -out GCF_015278285.1_ASM1527828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:47,404] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:47,408] [INFO] Selected 18 target genomes.
[2024-01-25 17:42:47,408] [INFO] Target genome list was writen to GCF_015278285.1_ASM1527828v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:47,423] [INFO] Task started: fastANI
[2024-01-25 17:42:47,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e109ec9-49af-4b69-9455-29b4449e8c01/GCF_015278285.1_ASM1527828v1_genomic.fna.gz --refList GCF_015278285.1_ASM1527828v1_genomic.fna/target_genomes.txt --output GCF_015278285.1_ASM1527828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:00,754] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:00,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:00,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:00,766] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:43:00,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:00,766] [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 invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	100.0	1187	1187	95	conclusive
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	99.9993	1186	1187	95	conclusive
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.8903	618	1187	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.8176	630	1187	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.6643	595	1187	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	81.6479	548	1187	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	81.5995	547	1187	95	below_threshold
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	81.52	571	1187	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.096	565	1187	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.9745	612	1187	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.8852	604	1187	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.7687	562	1187	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.7382	628	1187	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.7246	612	1187	95	below_threshold
Microbacterium marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	80.6439	527	1187	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.5682	549	1187	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.563	550	1187	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.4843	620	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:00,768] [INFO] DFAST Taxonomy check result was written to GCF_015278285.1_ASM1527828v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:00,768] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:00,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:00,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/checkm_data
[2024-01-25 17:43:00,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:00,807] [INFO] Task started: CheckM
[2024-01-25 17:43:00,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015278285.1_ASM1527828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015278285.1_ASM1527828v1_genomic.fna/checkm_input GCF_015278285.1_ASM1527828v1_genomic.fna/checkm_result
[2024-01-25 17:43:57,543] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:57,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:57,565] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:57,565] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:57,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015278285.1_ASM1527828v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:57,567] [INFO] Task started: Blastn
[2024-01-25 17:43:57,567] [INFO] Running command: blastn -query GCF_015278285.1_ASM1527828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a4eed2-43fa-4c67-a550-64ac23e61f78/dqc_reference/reference_markers_gtdb.fasta -out GCF_015278285.1_ASM1527828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:59,618] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:59,627] [INFO] Selected 18 target genomes.
[2024-01-25 17:43:59,627] [INFO] Target genome list was writen to GCF_015278285.1_ASM1527828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:59,648] [INFO] Task started: fastANI
[2024-01-25 17:43:59,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e109ec9-49af-4b69-9455-29b4449e8c01/GCF_015278285.1_ASM1527828v1_genomic.fna.gz --refList GCF_015278285.1_ASM1527828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015278285.1_ASM1527828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:13,526] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:13,537] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:13,538] [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
GCA_014197265.1	s__Microbacterium invictum	99.9992	1186	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007992455.1	s__Microbacterium saccharophilum	81.8183	630	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.54	98.03	0.93	0.90	5	-
GCA_900078385.1	s__Microbacterium sp900078385	81.7424	629	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	81.6987	605	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	81.6521	596	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCF_006716815.1	s__Microbacterium lacticum	81.5684	567	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCF_016807485.1	s__Microbacterium sp016807485	81.449	376	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	80.953	614	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	80.8818	559	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	80.8682	606	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	80.8618	597	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001314225.1	s__Microbacterium sp001314225	80.7494	591	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	80.732	629	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	80.7208	613	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204835.1	s__Microbacterium marinum	80.6333	525	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.15	96.15	0.88	0.88	2	-
GCF_011759705.1	s__Microbacterium ulmi	80.5574	550	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015278355.1	s__Microbacterium yannicii_B	80.5398	610	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409015.1	s__Microbacterium sp013409015	80.3575	563	1187	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 17:44:13,539] [INFO] GTDB search result was written to GCF_015278285.1_ASM1527828v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:13,539] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:13,542] [INFO] DFAST_QC result json was written to GCF_015278285.1_ASM1527828v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:13,543] [INFO] DFAST_QC completed!
[2024-01-25 17:44:13,543] [INFO] Total running time: 0h1m38s