[2024-01-24 10:57:39,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference
[2024-01-24 10:57:40,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,353] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d037af4-9e49-4f73-8ad1-56545039cc0f/GCF_017813355.1_ASM1781335v1_genomic.fna.gz | prodigal -d GCF_017813355.1_ASM1781335v1_genomic.fna/cds.fna -a GCF_017813355.1_ASM1781335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:54,102] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:54,102] [INFO] Task started: HMMsearch
[2024-01-24 10:57:54,102] [INFO] Running command: hmmsearch --tblout GCF_017813355.1_ASM1781335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/reference_markers.hmm GCF_017813355.1_ASM1781335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:54,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:54,413] [INFO] Found 6/6 markers.
[2024-01-24 10:57:54,456] [INFO] Query marker FASTA was written to GCF_017813355.1_ASM1781335v1_genomic.fna/markers.fasta
[2024-01-24 10:57:54,456] [INFO] Task started: Blastn
[2024-01-24 10:57:54,456] [INFO] Running command: blastn -query GCF_017813355.1_ASM1781335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/reference_markers.fasta -out GCF_017813355.1_ASM1781335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:55,377] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:55,381] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:55,381] [INFO] Target genome list was writen to GCF_017813355.1_ASM1781335v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:55,413] [INFO] Task started: fastANI
[2024-01-24 10:57:55,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d037af4-9e49-4f73-8ad1-56545039cc0f/GCF_017813355.1_ASM1781335v1_genomic.fna.gz --refList GCF_017813355.1_ASM1781335v1_genomic.fna/target_genomes.txt --output GCF_017813355.1_ASM1781335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:17,932] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:17,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:17,950] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:17,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:17,950] [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 rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	91.1276	1122	1630	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	84.8379	1196	1630	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	84.8353	1090	1630	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	82.5663	1156	1630	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.7609	863	1630	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	79.3559	869	1630	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.0498	783	1630	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	78.9792	833	1630	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	78.7933	768	1630	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.709	666	1630	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5915	679	1630	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.5029	715	1630	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.4093	684	1630	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.2534	618	1630	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	75.5533	222	1630	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	75.5182	229	1630	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	75.5133	230	1630	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	75.5117	231	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,952] [INFO] DFAST Taxonomy check result was written to GCF_017813355.1_ASM1781335v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:17,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:17,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:17,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/checkm_data
[2024-01-24 10:58:17,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:18,014] [INFO] Task started: CheckM
[2024-01-24 10:58:18,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813355.1_ASM1781335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813355.1_ASM1781335v1_genomic.fna/checkm_input GCF_017813355.1_ASM1781335v1_genomic.fna/checkm_result
[2024-01-24 10:59:27,931] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:27,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:27,951] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:27,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:27,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813355.1_ASM1781335v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:27,953] [INFO] Task started: Blastn
[2024-01-24 10:59:27,953] [INFO] Running command: blastn -query GCF_017813355.1_ASM1781335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7241df70-f651-4c3e-bfe7-4fcebf0319bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813355.1_ASM1781335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:29,368] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:29,373] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:29,373] [INFO] Target genome list was writen to GCF_017813355.1_ASM1781335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:29,384] [INFO] Task started: fastANI
[2024-01-24 10:59:29,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d037af4-9e49-4f73-8ad1-56545039cc0f/GCF_017813355.1_ASM1781335v1_genomic.fna.gz --refList GCF_017813355.1_ASM1781335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813355.1_ASM1781335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:47,637] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:47,648] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:47,648] [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_017813355.1	s__Roseomonas_B sp017813355	100.0	1630	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016106015.1	s__Roseomonas_B sp016106015	91.1104	1124	1630	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	85.0802	1017	1630	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_014199195.1	s__Roseomonas_B alkaliterrae	84.8356	1090	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_012163135.1	s__Roseomonas_B oryzicola	84.8297	1198	1630	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_005222755.1	s__Roseomonas_B sp005222755	84.8119	1182	1630	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_018129065.1	s__Roseomonas_B soli	84.422	1104	1630	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	84.3847	1182	1630	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	84.3618	1155	1630	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	84.0392	1111	1630	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	82.358	1068	1630	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_007129775.1	s__Rhodobaculum sp007129775	75.2681	125	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:47,650] [INFO] GTDB search result was written to GCF_017813355.1_ASM1781335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:47,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:47,654] [INFO] DFAST_QC result json was written to GCF_017813355.1_ASM1781335v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:47,654] [INFO] DFAST_QC completed!
[2024-01-24 10:59:47,654] [INFO] Total running time: 0h2m9s