[2024-01-25 18:16:50,809] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:50,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:50,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference
[2024-01-25 18:16:51,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:51,976] [INFO] Task started: Prodigal
[2024-01-25 18:16:51,976] [INFO] Running command: gunzip -c /var/lib/cwl/stgc40f499f-fff9-451d-bddb-0fc3692f4610/GCF_009735645.1_ASM973564v1_genomic.fna.gz | prodigal -d GCF_009735645.1_ASM973564v1_genomic.fna/cds.fna -a GCF_009735645.1_ASM973564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:59,512] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:59,513] [INFO] Task started: HMMsearch
[2024-01-25 18:16:59,513] [INFO] Running command: hmmsearch --tblout GCF_009735645.1_ASM973564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/reference_markers.hmm GCF_009735645.1_ASM973564v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:59,722] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:59,723] [INFO] Found 6/6 markers.
[2024-01-25 18:16:59,752] [INFO] Query marker FASTA was written to GCF_009735645.1_ASM973564v1_genomic.fna/markers.fasta
[2024-01-25 18:16:59,753] [INFO] Task started: Blastn
[2024-01-25 18:16:59,753] [INFO] Running command: blastn -query GCF_009735645.1_ASM973564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/reference_markers.fasta -out GCF_009735645.1_ASM973564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:00,918] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:00,921] [INFO] Selected 18 target genomes.
[2024-01-25 18:17:00,921] [INFO] Target genome list was writen to GCF_009735645.1_ASM973564v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:00,942] [INFO] Task started: fastANI
[2024-01-25 18:17:00,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgc40f499f-fff9-451d-bddb-0fc3692f4610/GCF_009735645.1_ASM973564v1_genomic.fna.gz --refList GCF_009735645.1_ASM973564v1_genomic.fna/target_genomes.txt --output GCF_009735645.1_ASM973564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:13,526] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:13,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:13,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:13,538] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:13,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:13,539] [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 oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	100.0	1012	1013	95	conclusive
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.6847	520	1013	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.594	517	1013	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	81.5705	519	1013	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	80.9168	533	1013	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	80.8046	507	1013	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	80.7619	485	1013	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.5345	477	1013	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.1186	466	1013	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.0565	504	1013	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	79.9335	475	1013	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.8802	449	1013	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	79.862	472	1013	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	79.7815	453	1013	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.7737	450	1013	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	79.4682	410	1013	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.7826	416	1013	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.5841	397	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:13,540] [INFO] DFAST Taxonomy check result was written to GCF_009735645.1_ASM973564v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:13,541] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:13,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:13,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/checkm_data
[2024-01-25 18:17:13,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:13,573] [INFO] Task started: CheckM
[2024-01-25 18:17:13,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009735645.1_ASM973564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009735645.1_ASM973564v1_genomic.fna/checkm_input GCF_009735645.1_ASM973564v1_genomic.fna/checkm_result
[2024-01-25 18:18:00,905] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:00,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:00,928] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:00,928] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:00,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009735645.1_ASM973564v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:00,930] [INFO] Task started: Blastn
[2024-01-25 18:18:00,930] [INFO] Running command: blastn -query GCF_009735645.1_ASM973564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f1400-37c7-481d-8b52-bcba67cdfb11/dqc_reference/reference_markers_gtdb.fasta -out GCF_009735645.1_ASM973564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:02,944] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:02,947] [INFO] Selected 14 target genomes.
[2024-01-25 18:18:02,947] [INFO] Target genome list was writen to GCF_009735645.1_ASM973564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:02,968] [INFO] Task started: fastANI
[2024-01-25 18:18:02,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgc40f499f-fff9-451d-bddb-0fc3692f4610/GCF_009735645.1_ASM973564v1_genomic.fna.gz --refList GCF_009735645.1_ASM973564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009735645.1_ASM973564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:13,940] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:13,949] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:13,950] [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_009735645.1	s__Microbacterium oryzae	100.0	1012	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001426925.1	s__Microbacterium sp001426925	81.6893	522	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_004564075.1	s__Microbacterium sediminis	81.6439	520	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_015235415.1	s__Microbacterium paludicola_A	81.5762	524	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016805985.1	s__Microbacterium sp016805985	81.3677	548	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592545.1	s__Microbacterium sp017592545	80.7748	509	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643695.1	s__Microbacterium album	80.7702	484	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326725.1	s__Microbacterium excoecariae	80.4199	484	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_014208045.1	s__Microbacterium thalassium	80.1747	482	1013	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	79.9228	476	1013	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	79.9102	467	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCF_011759705.1	s__Microbacterium ulmi	79.7863	453	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005347485.1	s__Microbacterium sp005347485	79.5155	427	1013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422405.1	s__Microbacterium luticocti	79.4797	409	1013	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 18:18:13,951] [INFO] GTDB search result was written to GCF_009735645.1_ASM973564v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:13,951] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:13,954] [INFO] DFAST_QC result json was written to GCF_009735645.1_ASM973564v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:13,955] [INFO] DFAST_QC completed!
[2024-01-25 18:18:13,955] [INFO] Total running time: 0h1m23s