[2024-01-24 13:40:35,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference
[2024-01-24 13:40:36,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,458] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a3010de-3c5f-45fd-a2e9-b41d3ee59e94/GCF_017654485.1_ASM1765448v1_genomic.fna.gz | prodigal -d GCF_017654485.1_ASM1765448v1_genomic.fna/cds.fna -a GCF_017654485.1_ASM1765448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,066] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,067] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,067] [INFO] Running command: hmmsearch --tblout GCF_017654485.1_ASM1765448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/reference_markers.hmm GCF_017654485.1_ASM1765448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,376] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,421] [INFO] Query marker FASTA was written to GCF_017654485.1_ASM1765448v1_genomic.fna/markers.fasta
[2024-01-24 13:40:51,421] [INFO] Task started: Blastn
[2024-01-24 13:40:51,422] [INFO] Running command: blastn -query GCF_017654485.1_ASM1765448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/reference_markers.fasta -out GCF_017654485.1_ASM1765448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,469] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:52,469] [INFO] Target genome list was writen to GCF_017654485.1_ASM1765448v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,475] [INFO] Task started: fastANI
[2024-01-24 13:40:52,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3010de-3c5f-45fd-a2e9-b41d3ee59e94/GCF_017654485.1_ASM1765448v1_genomic.fna.gz --refList GCF_017654485.1_ASM1765448v1_genomic.fna/target_genomes.txt --output GCF_017654485.1_ASM1765448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,768] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:04,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,768] [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 marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	100.0	1606	1607	95	conclusive
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	86.2782	1192	1607	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	86.206	987	1607	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	83.0371	953	1607	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	82.7797	974	1607	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	81.9285	775	1607	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	81.8638	836	1607	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5359	531	1607	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.5248	469	1607	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.2438	552	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,770] [INFO] DFAST Taxonomy check result was written to GCF_017654485.1_ASM1765448v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/checkm_data
[2024-01-24 13:41:04,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,819] [INFO] Task started: CheckM
[2024-01-24 13:41:04,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017654485.1_ASM1765448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017654485.1_ASM1765448v1_genomic.fna/checkm_input GCF_017654485.1_ASM1765448v1_genomic.fna/checkm_result
[2024-01-24 13:41:56,062] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:56,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,084] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:56,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:56,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017654485.1_ASM1765448v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:56,085] [INFO] Task started: Blastn
[2024-01-24 13:41:56,085] [INFO] Running command: blastn -query GCF_017654485.1_ASM1765448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb39452e-2e9a-42b8-9a49-94d8419aedd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017654485.1_ASM1765448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:57,726] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:57,730] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:57,730] [INFO] Target genome list was writen to GCF_017654485.1_ASM1765448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:57,735] [INFO] Task started: fastANI
[2024-01-24 13:41:57,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3010de-3c5f-45fd-a2e9-b41d3ee59e94/GCF_017654485.1_ASM1765448v1_genomic.fna.gz --refList GCF_017654485.1_ASM1765448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017654485.1_ASM1765448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:07,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,192] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:07,192] [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_017654485.1	s__Roseomonas sp017654485	100.0	1606	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.93	99.93	0.97	0.97	2	conclusive
GCF_003696345.1	s__Roseomonas sp003696345	86.3129	1186	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014490445.1	s__Roseomonas ludipueritiae	86.2083	987	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	83.0539	953	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355405.1	s__Roseomonas sp017355405	82.7533	974	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000245075.1	s__Roseomonas sp000245075	82.4385	869	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	81.9156	776	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,194] [INFO] GTDB search result was written to GCF_017654485.1_ASM1765448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:07,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:07,197] [INFO] DFAST_QC result json was written to GCF_017654485.1_ASM1765448v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:07,197] [INFO] DFAST_QC completed!
[2024-01-24 13:42:07,197] [INFO] Total running time: 0h1m32s