[2024-01-25 19:01:05,744] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:05,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:05,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference
[2024-01-25 19:01:06,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:06,875] [INFO] Task started: Prodigal
[2024-01-25 19:01:06,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ab9bae2-34bf-46fc-9d98-a578538f01e4/GCF_014199195.1_ASM1419919v1_genomic.fna.gz | prodigal -d GCF_014199195.1_ASM1419919v1_genomic.fna/cds.fna -a GCF_014199195.1_ASM1419919v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:17,537] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:17,537] [INFO] Task started: HMMsearch
[2024-01-25 19:01:17,537] [INFO] Running command: hmmsearch --tblout GCF_014199195.1_ASM1419919v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/reference_markers.hmm GCF_014199195.1_ASM1419919v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:17,760] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:17,761] [INFO] Found 6/6 markers.
[2024-01-25 19:01:17,798] [INFO] Query marker FASTA was written to GCF_014199195.1_ASM1419919v1_genomic.fna/markers.fasta
[2024-01-25 19:01:17,799] [INFO] Task started: Blastn
[2024-01-25 19:01:17,799] [INFO] Running command: blastn -query GCF_014199195.1_ASM1419919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/reference_markers.fasta -out GCF_014199195.1_ASM1419919v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:18,685] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:18,689] [INFO] Selected 16 target genomes.
[2024-01-25 19:01:18,689] [INFO] Target genome list was writen to GCF_014199195.1_ASM1419919v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:18,703] [INFO] Task started: fastANI
[2024-01-25 19:01:18,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab9bae2-34bf-46fc-9d98-a578538f01e4/GCF_014199195.1_ASM1419919v1_genomic.fna.gz --refList GCF_014199195.1_ASM1419919v1_genomic.fna/target_genomes.txt --output GCF_014199195.1_ASM1419919v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:38,422] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:38,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:38,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:38,433] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:38,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:38,433] [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
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	100.0	1386	1388	95	conclusive
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	84.808	1086	1388	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	84.7536	875	1388	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	82.4212	1076	1388	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.9323	695	1388	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.9271	785	1388	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.7115	672	1388	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	79.3605	813	1388	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	79.2932	596	1388	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	79.1766	776	1388	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	79.1535	612	1388	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	79.0959	664	1388	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	79.0634	724	1388	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.8805	623	1388	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.4879	589	1388	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.4286	626	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:38,434] [INFO] DFAST Taxonomy check result was written to GCF_014199195.1_ASM1419919v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:38,435] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:38,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:38,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/checkm_data
[2024-01-25 19:01:38,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:38,478] [INFO] Task started: CheckM
[2024-01-25 19:01:38,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199195.1_ASM1419919v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199195.1_ASM1419919v1_genomic.fna/checkm_input GCF_014199195.1_ASM1419919v1_genomic.fna/checkm_result
[2024-01-25 19:02:45,454] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:45,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:45,471] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:45,471] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:45,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199195.1_ASM1419919v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:45,472] [INFO] Task started: Blastn
[2024-01-25 19:02:45,472] [INFO] Running command: blastn -query GCF_014199195.1_ASM1419919v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacd6dd3c-fe41-4c46-9525-ebd0027dc415/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199195.1_ASM1419919v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:47,276] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:47,279] [INFO] Selected 10 target genomes.
[2024-01-25 19:02:47,279] [INFO] Target genome list was writen to GCF_014199195.1_ASM1419919v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:47,295] [INFO] Task started: fastANI
[2024-01-25 19:02:47,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab9bae2-34bf-46fc-9d98-a578538f01e4/GCF_014199195.1_ASM1419919v1_genomic.fna.gz --refList GCF_014199195.1_ASM1419919v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199195.1_ASM1419919v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:01,355] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:01,362] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:01,362] [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_014199195.1	s__Roseomonas_B alkaliterrae	100.0	1386	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	conclusive
GCF_017813355.1	s__Roseomonas_B sp017813355	84.9982	1082	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	84.8782	1102	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163135.1	s__Roseomonas_B oryzicola	84.827	1084	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018129065.1	s__Roseomonas_B soli	84.728	1015	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106015.1	s__Roseomonas_B sp016106015	84.7237	877	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	84.6721	943	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927745.1	s__Roseomonas_B sp012927745	84.3985	1065	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	83.4389	989	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129025.1	s__Roseomonas_B terrae	82.5533	1009	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:01,364] [INFO] GTDB search result was written to GCF_014199195.1_ASM1419919v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:01,364] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:01,367] [INFO] DFAST_QC result json was written to GCF_014199195.1_ASM1419919v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:01,367] [INFO] DFAST_QC completed!
[2024-01-25 19:03:01,367] [INFO] Total running time: 0h1m56s