[2024-01-24 13:41:18,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference
[2024-01-24 13:41:20,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,091] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,092] [INFO] Running command: gunzip -c /var/lib/cwl/stg3202023d-4902-4d93-8463-3f08c8a01c25/GCF_014204835.1_ASM1420483v1_genomic.fna.gz | prodigal -d GCF_014204835.1_ASM1420483v1_genomic.fna/cds.fna -a GCF_014204835.1_ASM1420483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:29,178] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:29,179] [INFO] Task started: HMMsearch
[2024-01-24 13:41:29,179] [INFO] Running command: hmmsearch --tblout GCF_014204835.1_ASM1420483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/reference_markers.hmm GCF_014204835.1_ASM1420483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:29,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:29,478] [INFO] Found 6/6 markers.
[2024-01-24 13:41:29,521] [INFO] Query marker FASTA was written to GCF_014204835.1_ASM1420483v1_genomic.fna/markers.fasta
[2024-01-24 13:41:29,521] [INFO] Task started: Blastn
[2024-01-24 13:41:29,522] [INFO] Running command: blastn -query GCF_014204835.1_ASM1420483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/reference_markers.fasta -out GCF_014204835.1_ASM1420483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:30,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:30,805] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:30,806] [INFO] Target genome list was writen to GCF_014204835.1_ASM1420483v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:30,808] [INFO] Task started: fastANI
[2024-01-24 13:41:30,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg3202023d-4902-4d93-8463-3f08c8a01c25/GCF_014204835.1_ASM1420483v1_genomic.fna.gz --refList GCF_014204835.1_ASM1420483v1_genomic.fna/target_genomes.txt --output GCF_014204835.1_ASM1420483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:44,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:44,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:44,790] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:44,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:44,791] [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 marinum	strain=DSM 24947	GCA_014204835.1	421115	421115	type	True	100.0	1040	1041	95	conclusive
Microbacterium oleivorans	strain=NBRC 103075	GCA_001552475.1	273677	273677	suspected-type	True	82.5175	626	1041	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.3224	561	1041	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.2622	550	1041	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.2374	550	1041	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	81.2286	530	1041	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.9699	527	1041	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.9633	532	1041	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	80.9388	519	1041	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	80.7868	498	1041	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.7621	509	1041	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.7024	519	1041	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.4028	497	1041	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.3947	513	1041	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.3939	493	1041	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.393	520	1041	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.349	508	1041	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.3079	497	1041	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.1794	517	1041	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.1104	505	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,792] [INFO] DFAST Taxonomy check result was written to GCF_014204835.1_ASM1420483v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:44,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:44,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:44,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/checkm_data
[2024-01-24 13:41:44,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:44,827] [INFO] Task started: CheckM
[2024-01-24 13:41:44,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204835.1_ASM1420483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204835.1_ASM1420483v1_genomic.fna/checkm_input GCF_014204835.1_ASM1420483v1_genomic.fna/checkm_result
[2024-01-24 13:42:40,815] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:40,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:40,837] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:40,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:40,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204835.1_ASM1420483v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:40,838] [INFO] Task started: Blastn
[2024-01-24 13:42:40,839] [INFO] Running command: blastn -query GCF_014204835.1_ASM1420483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a7f2bff-c904-44ac-85f4-fb8c422f173e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204835.1_ASM1420483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:42,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:42,771] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:42,772] [INFO] Target genome list was writen to GCF_014204835.1_ASM1420483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:42,780] [INFO] Task started: fastANI
[2024-01-24 13:42:42,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg3202023d-4902-4d93-8463-3f08c8a01c25/GCF_014204835.1_ASM1420483v1_genomic.fna.gz --refList GCF_014204835.1_ASM1420483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204835.1_ASM1420483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:50,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:50,674] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:50,674] [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_014204835.1	s__Microbacterium marinum	100.0	1040	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.15	96.15	0.88	0.88	2	conclusive
GCF_001644225.1	s__Microbacterium oleivorans_A	83.8862	675	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102005.1	s__Microbacterium sp900102005	83.0749	643	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.39	98.39	0.95	0.95	2	-
GCF_001691565.1	s__Microbacterium oleivorans_B	83.0712	631	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383475.1	s__Microbacterium sp000383475	83.0562	645	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.27	98.25	0.96	0.95	4	-
GCF_001552475.1	s__Microbacterium oleivorans	82.5046	627	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.13	99.05	0.96	0.96	4	-
GCF_003651225.1	s__Microbacterium telephonicum	81.2935	564	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	81.22	556	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898315.1	s__Microbacterium sp001898315	80.8278	512	1041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_016907295.1	s__Microbacterium dextranolyticum	80.7654	500	1041	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	80.5258	494	1041	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 13:42:50,676] [INFO] GTDB search result was written to GCF_014204835.1_ASM1420483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:50,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:50,680] [INFO] DFAST_QC result json was written to GCF_014204835.1_ASM1420483v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:50,681] [INFO] DFAST_QC completed!
[2024-01-24 13:42:50,681] [INFO] Total running time: 0h1m32s