[2024-01-24 12:46:53,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:53,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:53,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference
[2024-01-24 12:46:55,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:55,073] [INFO] Task started: Prodigal
[2024-01-24 12:46:55,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bbf075e-4c79-4b6c-8a4e-6dcc136f3045/GCF_007559335.1_ASM755933v1_genomic.fna.gz | prodigal -d GCF_007559335.1_ASM755933v1_genomic.fna/cds.fna -a GCF_007559335.1_ASM755933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:22,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:22,030] [INFO] Task started: HMMsearch
[2024-01-24 12:47:22,030] [INFO] Running command: hmmsearch --tblout GCF_007559335.1_ASM755933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/reference_markers.hmm GCF_007559335.1_ASM755933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:22,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:22,312] [INFO] Found 6/6 markers.
[2024-01-24 12:47:22,351] [INFO] Query marker FASTA was written to GCF_007559335.1_ASM755933v1_genomic.fna/markers.fasta
[2024-01-24 12:47:22,352] [INFO] Task started: Blastn
[2024-01-24 12:47:22,352] [INFO] Running command: blastn -query GCF_007559335.1_ASM755933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/reference_markers.fasta -out GCF_007559335.1_ASM755933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:23,054] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:23,059] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:23,060] [INFO] Target genome list was writen to GCF_007559335.1_ASM755933v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:23,071] [INFO] Task started: fastANI
[2024-01-24 12:47:23,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bbf075e-4c79-4b6c-8a4e-6dcc136f3045/GCF_007559335.1_ASM755933v1_genomic.fna.gz --refList GCF_007559335.1_ASM755933v1_genomic.fna/target_genomes.txt --output GCF_007559335.1_ASM755933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:30,102] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:30,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:30,115] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:30,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:30,115] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	100.0	1377	1377	95	conclusive
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	78.6812	346	1377	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.9629	262	1377	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.7126	176	1377	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.3046	143	1377	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.8754	209	1377	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	76.8222	111	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,118] [INFO] DFAST Taxonomy check result was written to GCF_007559335.1_ASM755933v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:30,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:30,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:30,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/checkm_data
[2024-01-24 12:47:30,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:30,163] [INFO] Task started: CheckM
[2024-01-24 12:47:30,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007559335.1_ASM755933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007559335.1_ASM755933v1_genomic.fna/checkm_input GCF_007559335.1_ASM755933v1_genomic.fna/checkm_result
[2024-01-24 12:48:42,065] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:42,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:42,085] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:42,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:42,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007559335.1_ASM755933v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:42,086] [INFO] Task started: Blastn
[2024-01-24 12:48:42,086] [INFO] Running command: blastn -query GCF_007559335.1_ASM755933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753f9d3c-4fa4-42e4-9408-5226351ffe32/dqc_reference/reference_markers_gtdb.fasta -out GCF_007559335.1_ASM755933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:43,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:43,335] [INFO] Selected 14 target genomes.
[2024-01-24 12:48:43,335] [INFO] Target genome list was writen to GCF_007559335.1_ASM755933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:43,378] [INFO] Task started: fastANI
[2024-01-24 12:48:43,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bbf075e-4c79-4b6c-8a4e-6dcc136f3045/GCF_007559335.1_ASM755933v1_genomic.fna.gz --refList GCF_007559335.1_ASM755933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007559335.1_ASM755933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:54,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:54,291] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:54,291] [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_007559335.1	s__Rariglobus hedericola	100.0	1377	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002382525.1	s__Rariglobus sp002382525	81.1854	514	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.24	99.24	0.83	0.83	2	-
GCA_903876795.1	s__Rariglobus sp903876795	81.0581	485	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904685.1	s__Rariglobus sp903904685	79.754	374	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.84	99.84	0.96	0.96	2	-
GCA_000972765.1	s__IMCC26134_A sp000972765	78.9912	272	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	99.41	99.35	0.95	0.94	9	-
GCF_002310495.1	s__Nibricoccus aquaticus	78.6934	345	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000242935.3	s__Geminisphaera sp000242935	78.0284	350	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_903948415.1	s__CAITWF01 sp903948415	77.9982	272	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	77.8488	234	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650175.1	s__Ereboglobus sp001650175	77.6976	287	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	77.6198	155	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871755.1	s__UBA6669 sp016871755	77.471	176	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217595.1	s__MWDT01 sp016217595	77.1846	163	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862595.1	s__UBA6669 sp903862595	77.0973	173	1377	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:54,293] [INFO] GTDB search result was written to GCF_007559335.1_ASM755933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:54,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:54,296] [INFO] DFAST_QC result json was written to GCF_007559335.1_ASM755933v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:54,296] [INFO] DFAST_QC completed!
[2024-01-24 12:48:54,296] [INFO] Total running time: 0h2m0s