[2024-01-24 15:18:19,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference
[2024-01-24 15:18:20,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,689] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bc4a0de-d2f1-4f4c-8eda-6ae3cfa33f1f/GCF_017355885.1_ASM1735588v1_genomic.fna.gz | prodigal -d GCF_017355885.1_ASM1735588v1_genomic.fna/cds.fna -a GCF_017355885.1_ASM1735588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:35,804] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:35,804] [INFO] Task started: HMMsearch
[2024-01-24 15:18:35,805] [INFO] Running command: hmmsearch --tblout GCF_017355885.1_ASM1735588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/reference_markers.hmm GCF_017355885.1_ASM1735588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:36,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:36,097] [INFO] Found 6/6 markers.
[2024-01-24 15:18:36,161] [INFO] Query marker FASTA was written to GCF_017355885.1_ASM1735588v1_genomic.fna/markers.fasta
[2024-01-24 15:18:36,162] [INFO] Task started: Blastn
[2024-01-24 15:18:36,162] [INFO] Running command: blastn -query GCF_017355885.1_ASM1735588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/reference_markers.fasta -out GCF_017355885.1_ASM1735588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:37,068] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:37,071] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:37,071] [INFO] Target genome list was writen to GCF_017355885.1_ASM1735588v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:37,078] [INFO] Task started: fastANI
[2024-01-24 15:18:37,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc4a0de-d2f1-4f4c-8eda-6ae3cfa33f1f/GCF_017355885.1_ASM1735588v1_genomic.fna.gz --refList GCF_017355885.1_ASM1735588v1_genomic.fna/target_genomes.txt --output GCF_017355885.1_ASM1735588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:52,576] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:52,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:52,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:52,592] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:52,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:52,593] [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
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	80.5049	704	1642	95	below_threshold
Roseococcus suduntuyensis	strain=DSM 19979	GCA_014196305.1	455361	455361	type	True	80.392	702	1642	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	80.3651	699	1642	95	below_threshold
Roseococcus suduntuyensis	strain=SHET	GCA_017311525.1	455361	455361	type	True	80.3294	704	1642	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	79.7829	700	1642	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.1673	626	1642	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.8591	593	1642	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.7786	524	1642	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	78.6127	525	1642	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	78.5786	528	1642	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.5222	628	1642	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	78.5026	622	1642	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.4913	488	1642	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.491	583	1642	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	78.3493	547	1642	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.0581	521	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:52,595] [INFO] DFAST Taxonomy check result was written to GCF_017355885.1_ASM1735588v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:52,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:52,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:52,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/checkm_data
[2024-01-24 15:18:52,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:52,652] [INFO] Task started: CheckM
[2024-01-24 15:18:52,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017355885.1_ASM1735588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017355885.1_ASM1735588v1_genomic.fna/checkm_input GCF_017355885.1_ASM1735588v1_genomic.fna/checkm_result
[2024-01-24 15:19:41,321] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:41,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:41,344] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:41,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:41,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017355885.1_ASM1735588v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:41,345] [INFO] Task started: Blastn
[2024-01-24 15:19:41,345] [INFO] Running command: blastn -query GCF_017355885.1_ASM1735588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2e87e7d-8a43-40cf-b8a2-d3ea9199f4b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017355885.1_ASM1735588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:43,018] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:43,022] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:43,022] [INFO] Target genome list was writen to GCF_017355885.1_ASM1735588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:43,032] [INFO] Task started: fastANI
[2024-01-24 15:19:43,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc4a0de-d2f1-4f4c-8eda-6ae3cfa33f1f/GCF_017355885.1_ASM1735588v1_genomic.fna.gz --refList GCF_017355885.1_ASM1735588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017355885.1_ASM1735588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:56,087] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:56,103] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:56,103] [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_017355885.1	s__Roseococcus sp017355885	100.0	1640	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425365.1	s__Roseococcus flocculans	80.7653	711	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764365.1	s__Roseococcus sp014764365	80.5237	702	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083995.1	s__Roseococcus sp019083995	80.4475	772	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196305.1	s__Roseococcus suduntuyensis	80.3465	709	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017311575.1	s__Roseococcus thiosulfatophilus	80.3148	705	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	80.174	330	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336745.1	s__Roseococcus sp004336745	79.9753	742	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413645.1	s__Roseococcus sp018413645	79.7917	697	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005855.1	s__Rhodovarius sp004005855	78.5283	626	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	78.4737	490	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	78.3854	543	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017355405.1	s__Roseomonas sp017355405	78.0257	525	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:56,104] [INFO] GTDB search result was written to GCF_017355885.1_ASM1735588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:56,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:56,109] [INFO] DFAST_QC result json was written to GCF_017355885.1_ASM1735588v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:56,109] [INFO] DFAST_QC completed!
[2024-01-24 15:19:56,109] [INFO] Total running time: 0h1m37s