[2024-01-24 13:25:29,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,995] [INFO] DQC Reference Directory: /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference
[2024-01-24 13:25:31,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,364] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg54633163-c07a-4dd9-83a2-df9f55fc3a4e/GCF_004564075.1_ASM456407v1_genomic.fna.gz | prodigal -d GCF_004564075.1_ASM456407v1_genomic.fna/cds.fna -a GCF_004564075.1_ASM456407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:40,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:40,054] [INFO] Task started: HMMsearch
[2024-01-24 13:25:40,054] [INFO] Running command: hmmsearch --tblout GCF_004564075.1_ASM456407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/reference_markers.hmm GCF_004564075.1_ASM456407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:40,308] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:40,310] [INFO] Found 6/6 markers.
[2024-01-24 13:25:40,338] [INFO] Query marker FASTA was written to GCF_004564075.1_ASM456407v1_genomic.fna/markers.fasta
[2024-01-24 13:25:40,338] [INFO] Task started: Blastn
[2024-01-24 13:25:40,338] [INFO] Running command: blastn -query GCF_004564075.1_ASM456407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/reference_markers.fasta -out GCF_004564075.1_ASM456407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:41,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:41,744] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:41,744] [INFO] Target genome list was writen to GCF_004564075.1_ASM456407v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:41,750] [INFO] Task started: fastANI
[2024-01-24 13:25:41,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg54633163-c07a-4dd9-83a2-df9f55fc3a4e/GCF_004564075.1_ASM456407v1_genomic.fna.gz --refList GCF_004564075.1_ASM456407v1_genomic.fna/target_genomes.txt --output GCF_004564075.1_ASM456407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:52,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:52,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:52,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:52,222] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:25:52,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:52,222] [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 sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	100.0	972	972	95	conclusive
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	99.9396	907	972	95	conclusive
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	99.9396	907	972	95	conclusive
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	81.6733	517	972	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	81.5471	585	972	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	81.5261	513	972	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	81.3611	532	972	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	81.0334	517	972	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.6973	475	972	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.5062	450	972	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	80.3473	415	972	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.3392	466	972	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.314	429	972	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.0946	449	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:52,224] [INFO] DFAST Taxonomy check result was written to GCF_004564075.1_ASM456407v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:52,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:52,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:52,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/checkm_data
[2024-01-24 13:25:52,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:52,260] [INFO] Task started: CheckM
[2024-01-24 13:25:52,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004564075.1_ASM456407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004564075.1_ASM456407v1_genomic.fna/checkm_input GCF_004564075.1_ASM456407v1_genomic.fna/checkm_result
[2024-01-24 13:26:41,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:41,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,021] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:41,021] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:41,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004564075.1_ASM456407v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:41,022] [INFO] Task started: Blastn
[2024-01-24 13:26:41,022] [INFO] Running command: blastn -query GCF_004564075.1_ASM456407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge594fdc2-ff79-4c55-a6f7-c18dc9bed987/dqc_reference/reference_markers_gtdb.fasta -out GCF_004564075.1_ASM456407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:43,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:43,518] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:43,518] [INFO] Target genome list was writen to GCF_004564075.1_ASM456407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:43,547] [INFO] Task started: fastANI
[2024-01-24 13:26:43,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg54633163-c07a-4dd9-83a2-df9f55fc3a4e/GCF_004564075.1_ASM456407v1_genomic.fna.gz --refList GCF_004564075.1_ASM456407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004564075.1_ASM456407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:53,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:53,561] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:53,561] [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_004564075.1	s__Microbacterium sediminis	100.0	972	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	conclusive
GCF_015235415.1	s__Microbacterium paludicola_A	82.6244	567	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001426925.1	s__Microbacterium sp001426925	82.5997	552	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_016805985.1	s__Microbacterium sp016805985	82.0739	594	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735645.1	s__Microbacterium oryzae	81.712	518	972	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	81.3539	540	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422385.1	s__Microbacterium indicum	81.228	496	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970975.1	s__Microbacterium halophytorum	81.0322	517	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	80.7636	470	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCA_001898315.1	s__Microbacterium sp001898315	80.3806	457	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_902506375.1	s__Microbacterium sp902506375	80.276	478	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409745.1	s__Microbacterium pseudoresistens	80.2671	418	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	79.234	437	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:53,563] [INFO] GTDB search result was written to GCF_004564075.1_ASM456407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:53,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:53,567] [INFO] DFAST_QC result json was written to GCF_004564075.1_ASM456407v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:53,567] [INFO] DFAST_QC completed!
[2024-01-24 13:26:53,568] [INFO] Total running time: 0h1m24s