[2024-01-24 14:55:07,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference
[2024-01-24 14:55:09,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,465] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg139715c9-1cb3-4ac3-b33e-7cd6e040e784/GCF_000971235.1_ASM97123v1_genomic.fna.gz | prodigal -d GCF_000971235.1_ASM97123v1_genomic.fna/cds.fna -a GCF_000971235.1_ASM97123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:18,537] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:18,537] [INFO] Task started: HMMsearch
[2024-01-24 14:55:18,537] [INFO] Running command: hmmsearch --tblout GCF_000971235.1_ASM97123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/reference_markers.hmm GCF_000971235.1_ASM97123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:18,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:18,811] [INFO] Found 6/6 markers.
[2024-01-24 14:55:18,842] [INFO] Query marker FASTA was written to GCF_000971235.1_ASM97123v1_genomic.fna/markers.fasta
[2024-01-24 14:55:18,842] [INFO] Task started: Blastn
[2024-01-24 14:55:18,842] [INFO] Running command: blastn -query GCF_000971235.1_ASM97123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/reference_markers.fasta -out GCF_000971235.1_ASM97123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:20,104] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:20,109] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:20,109] [INFO] Target genome list was writen to GCF_000971235.1_ASM97123v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:20,115] [INFO] Task started: fastANI
[2024-01-24 14:55:20,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg139715c9-1cb3-4ac3-b33e-7cd6e040e784/GCF_000971235.1_ASM97123v1_genomic.fna.gz --refList GCF_000971235.1_ASM97123v1_genomic.fna/target_genomes.txt --output GCF_000971235.1_ASM97123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:30,085] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:30,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:30,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:30,104] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:30,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:30,105] [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
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	100.0	1014	1015	95	conclusive
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	91.5494	871	1015	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	87.0983	776	1015	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	87.0433	794	1015	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	86.9064	789	1015	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	85.7813	744	1015	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	85.6318	766	1015	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	85.3715	718	1015	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.8629	353	1015	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.7334	433	1015	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.4664	264	1015	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.2695	312	1015	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.9291	271	1015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:30,107] [INFO] DFAST Taxonomy check result was written to GCF_000971235.1_ASM97123v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:30,114] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:30,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:30,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/checkm_data
[2024-01-24 14:55:30,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:30,152] [INFO] Task started: CheckM
[2024-01-24 14:55:30,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971235.1_ASM97123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971235.1_ASM97123v1_genomic.fna/checkm_input GCF_000971235.1_ASM97123v1_genomic.fna/checkm_result
[2024-01-24 14:56:04,887] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:04,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:04,905] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:04,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:04,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971235.1_ASM97123v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:04,907] [INFO] Task started: Blastn
[2024-01-24 14:56:04,907] [INFO] Running command: blastn -query GCF_000971235.1_ASM97123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfae68485-76dc-4f2c-9423-71e85f270bfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971235.1_ASM97123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:07,019] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:07,022] [INFO] Selected 9 target genomes.
[2024-01-24 14:56:07,023] [INFO] Target genome list was writen to GCF_000971235.1_ASM97123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:07,028] [INFO] Task started: fastANI
[2024-01-24 14:56:07,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg139715c9-1cb3-4ac3-b33e-7cd6e040e784/GCF_000971235.1_ASM97123v1_genomic.fna.gz --refList GCF_000971235.1_ASM97123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971235.1_ASM97123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:14,446] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:14,463] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:14,463] [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_000971235.1	s__Demequina subtropica	100.0	1014	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000971115.1	s__Demequina gelatinilytica	91.5494	871	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759715.1	s__Demequina mangrovi	87.1307	774	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971395.1	s__Demequina iriomotensis	86.9064	789	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971155.1	s__Demequina maris	85.7961	743	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971255.1	s__Demequina rhizosphaerae	85.6373	766	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_000971215.1	s__Demequina silvatica	85.4116	710	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	85.4019	716	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971135.1	s__Demequina phytophila	85.1019	714	1015	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:14,465] [INFO] GTDB search result was written to GCF_000971235.1_ASM97123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:14,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:14,470] [INFO] DFAST_QC result json was written to GCF_000971235.1_ASM97123v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:14,470] [INFO] DFAST_QC completed!
[2024-01-24 14:56:14,470] [INFO] Total running time: 0h1m7s