[2024-01-24 11:59:35,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,276] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,276] [INFO] DQC Reference Directory: /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference
[2024-01-24 11:59:36,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,537] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,537] [INFO] Running command: gunzip -c /var/lib/cwl/stge8d93a80-7e4f-45e0-8bfd-858933f0df87/GCF_018413645.1_ASM1841364v1_genomic.fna.gz | prodigal -d GCF_018413645.1_ASM1841364v1_genomic.fna/cds.fna -a GCF_018413645.1_ASM1841364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:50,056] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:50,056] [INFO] Task started: HMMsearch
[2024-01-24 11:59:50,056] [INFO] Running command: hmmsearch --tblout GCF_018413645.1_ASM1841364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/reference_markers.hmm GCF_018413645.1_ASM1841364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:50,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:50,396] [INFO] Found 6/6 markers.
[2024-01-24 11:59:50,445] [INFO] Query marker FASTA was written to GCF_018413645.1_ASM1841364v1_genomic.fna/markers.fasta
[2024-01-24 11:59:50,445] [INFO] Task started: Blastn
[2024-01-24 11:59:50,445] [INFO] Running command: blastn -query GCF_018413645.1_ASM1841364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/reference_markers.fasta -out GCF_018413645.1_ASM1841364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:51,233] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:51,237] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:51,238] [INFO] Target genome list was writen to GCF_018413645.1_ASM1841364v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:51,264] [INFO] Task started: fastANI
[2024-01-24 11:59:51,264] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d93a80-7e4f-45e0-8bfd-858933f0df87/GCF_018413645.1_ASM1841364v1_genomic.fna.gz --refList GCF_018413645.1_ASM1841364v1_genomic.fna/target_genomes.txt --output GCF_018413645.1_ASM1841364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:07,089] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:07,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:07,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:07,108] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:07,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:07,109] [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 pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	100.0	1588	1591	95	conclusive
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	80.5964	738	1591	95	below_threshold
Roseococcus suduntuyensis	strain=SHET	GCA_017311525.1	455361	455361	type	True	80.4868	756	1591	95	below_threshold
Roseococcus suduntuyensis	strain=DSM 19979	GCA_014196305.1	455361	455361	type	True	80.4681	754	1591	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	80.4451	765	1591	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	79.113	706	1591	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.0626	621	1591	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	79.0229	651	1591	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.8176	541	1591	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.5797	585	1591	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	78.5326	594	1591	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	78.2483	551	1591	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.1825	531	1591	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.7432	215	1591	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	75.2673	210	1591	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	75.2468	192	1591	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	75.1991	214	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:07,111] [INFO] DFAST Taxonomy check result was written to GCF_018413645.1_ASM1841364v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:07,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:07,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:07,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/checkm_data
[2024-01-24 12:00:07,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:07,163] [INFO] Task started: CheckM
[2024-01-24 12:00:07,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018413645.1_ASM1841364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018413645.1_ASM1841364v1_genomic.fna/checkm_input GCF_018413645.1_ASM1841364v1_genomic.fna/checkm_result
[2024-01-24 12:00:50,857] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:50,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:50,882] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:50,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:50,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018413645.1_ASM1841364v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:50,883] [INFO] Task started: Blastn
[2024-01-24 12:00:50,883] [INFO] Running command: blastn -query GCF_018413645.1_ASM1841364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2879f7-3da3-4ad2-8cf8-22e05fc7d397/dqc_reference/reference_markers_gtdb.fasta -out GCF_018413645.1_ASM1841364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:52,196] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:52,201] [INFO] Selected 15 target genomes.
[2024-01-24 12:00:52,201] [INFO] Target genome list was writen to GCF_018413645.1_ASM1841364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:52,216] [INFO] Task started: fastANI
[2024-01-24 12:00:52,216] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d93a80-7e4f-45e0-8bfd-858933f0df87/GCF_018413645.1_ASM1841364v1_genomic.fna.gz --refList GCF_018413645.1_ASM1841364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018413645.1_ASM1841364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:06,682] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:06,698] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:06,698] [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_018413645.1	s__Roseococcus sp018413645	100.0	1588	1591	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_004336745.1	s__Roseococcus sp004336745	85.8967	1132	1591	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	81.8221	886	1591	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	80.6023	738	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	80.5433	750	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196305.1	s__Roseococcus suduntuyensis	80.4768	753	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014764365.1	s__Roseococcus sp014764365	80.4271	767	1591	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	80.1586	354	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355885.1	s__Roseococcus sp017355885	79.7156	699	1591	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	79.1432	702	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	78.4061	664	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	75.3762	236	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	75.3347	243	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015159745.1	s__Ramlibacter aquaticus	75.2585	213	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	75.2276	197	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:06,700] [INFO] GTDB search result was written to GCF_018413645.1_ASM1841364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:06,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:06,705] [INFO] DFAST_QC result json was written to GCF_018413645.1_ASM1841364v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:06,705] [INFO] DFAST_QC completed!
[2024-01-24 12:01:06,705] [INFO] Total running time: 0h1m31s