[2024-01-25 17:45:50,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:50,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:50,657] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference
[2024-01-25 17:45:51,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:51,778] [INFO] Task started: Prodigal
[2024-01-25 17:45:51,778] [INFO] Running command: gunzip -c /var/lib/cwl/stga0617563-b626-4c42-a463-2d6eda0c7f60/GCF_017355405.1_ASM1735540v1_genomic.fna.gz | prodigal -d GCF_017355405.1_ASM1735540v1_genomic.fna/cds.fna -a GCF_017355405.1_ASM1735540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:05,548] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:05,548] [INFO] Task started: HMMsearch
[2024-01-25 17:46:05,548] [INFO] Running command: hmmsearch --tblout GCF_017355405.1_ASM1735540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/reference_markers.hmm GCF_017355405.1_ASM1735540v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:05,841] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:05,843] [INFO] Found 6/6 markers.
[2024-01-25 17:46:05,886] [INFO] Query marker FASTA was written to GCF_017355405.1_ASM1735540v1_genomic.fna/markers.fasta
[2024-01-25 17:46:05,887] [INFO] Task started: Blastn
[2024-01-25 17:46:05,887] [INFO] Running command: blastn -query GCF_017355405.1_ASM1735540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/reference_markers.fasta -out GCF_017355405.1_ASM1735540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:06,815] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:06,818] [INFO] Selected 9 target genomes.
[2024-01-25 17:46:06,818] [INFO] Target genome list was writen to GCF_017355405.1_ASM1735540v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:06,831] [INFO] Task started: fastANI
[2024-01-25 17:46:06,832] [INFO] Running command: fastANI --query /var/lib/cwl/stga0617563-b626-4c42-a463-2d6eda0c7f60/GCF_017355405.1_ASM1735540v1_genomic.fna.gz --refList GCF_017355405.1_ASM1735540v1_genomic.fna/target_genomes.txt --output GCF_017355405.1_ASM1735540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:18,454] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:18,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:18,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:18,462] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:18,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:18,462] [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 haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	100.0	1628	1630	95	conclusive
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	83.7994	1078	1630	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	83.5527	924	1630	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	82.8436	1029	1630	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	82.8011	946	1630	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	82.047	847	1630	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.2776	502	1630	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.215	621	1630	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.1348	559	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:18,463] [INFO] DFAST Taxonomy check result was written to GCF_017355405.1_ASM1735540v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:18,464] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:18,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:18,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/checkm_data
[2024-01-25 17:46:18,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:18,518] [INFO] Task started: CheckM
[2024-01-25 17:46:18,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017355405.1_ASM1735540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017355405.1_ASM1735540v1_genomic.fna/checkm_input GCF_017355405.1_ASM1735540v1_genomic.fna/checkm_result
[2024-01-25 17:47:43,572] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:43,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:43,590] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:43,590] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:43,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017355405.1_ASM1735540v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:43,591] [INFO] Task started: Blastn
[2024-01-25 17:47:43,591] [INFO] Running command: blastn -query GCF_017355405.1_ASM1735540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe652580-4862-4f30-83de-154b74e500bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_017355405.1_ASM1735540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:45,382] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:45,385] [INFO] Selected 8 target genomes.
[2024-01-25 17:47:45,386] [INFO] Target genome list was writen to GCF_017355405.1_ASM1735540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:45,391] [INFO] Task started: fastANI
[2024-01-25 17:47:45,391] [INFO] Running command: fastANI --query /var/lib/cwl/stga0617563-b626-4c42-a463-2d6eda0c7f60/GCF_017355405.1_ASM1735540v1_genomic.fna.gz --refList GCF_017355405.1_ASM1735540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017355405.1_ASM1735540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:56,825] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:56,831] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:56,831] [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_017355405.1	s__Roseomonas sp017355405	100.0	1628	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003696345.1	s__Roseomonas sp003696345	83.7235	1088	1630	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	83.4699	935	1630	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	82.8797	1027	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654485.1	s__Roseomonas sp017654485	82.8214	951	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.93	99.93	0.97	0.97	2	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	82.0575	846	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	81.9744	902	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000245075.1	s__Roseomonas sp000245075	81.4901	845	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:56,833] [INFO] GTDB search result was written to GCF_017355405.1_ASM1735540v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:56,834] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:56,836] [INFO] DFAST_QC result json was written to GCF_017355405.1_ASM1735540v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:56,836] [INFO] DFAST_QC completed!
[2024-01-25 17:47:56,836] [INFO] Total running time: 0h2m6s