[2024-01-24 13:18:32,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference
[2024-01-24 13:18:33,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,438] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg96336e0b-bc3d-4da6-b5e0-596c3e20b6c1/GCF_014490445.1_ASM1449044v1_genomic.fna.gz | prodigal -d GCF_014490445.1_ASM1449044v1_genomic.fna/cds.fna -a GCF_014490445.1_ASM1449044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:48,744] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:48,745] [INFO] Task started: HMMsearch
[2024-01-24 13:18:48,745] [INFO] Running command: hmmsearch --tblout GCF_014490445.1_ASM1449044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/reference_markers.hmm GCF_014490445.1_ASM1449044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:49,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:49,128] [INFO] Found 6/6 markers.
[2024-01-24 13:18:49,188] [INFO] Query marker FASTA was written to GCF_014490445.1_ASM1449044v1_genomic.fna/markers.fasta
[2024-01-24 13:18:49,189] [INFO] Task started: Blastn
[2024-01-24 13:18:49,189] [INFO] Running command: blastn -query GCF_014490445.1_ASM1449044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/reference_markers.fasta -out GCF_014490445.1_ASM1449044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,215] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,219] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:50,219] [INFO] Target genome list was writen to GCF_014490445.1_ASM1449044v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:50,226] [INFO] Task started: fastANI
[2024-01-24 13:18:50,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg96336e0b-bc3d-4da6-b5e0-596c3e20b6c1/GCF_014490445.1_ASM1449044v1_genomic.fna.gz --refList GCF_014490445.1_ASM1449044v1_genomic.fna/target_genomes.txt --output GCF_014490445.1_ASM1449044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:02,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:02,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:02,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:02,519] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:02,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:02,519] [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 ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	100.0	1578	1593	95	conclusive
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	91.5408	1285	1593	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	85.9146	1017	1593	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	83.5295	941	1593	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	83.4125	963	1593	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	82.0986	801	1593	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	81.6584	830	1593	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.6333	580	1593	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5593	506	1593	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.4223	468	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:02,523] [INFO] DFAST Taxonomy check result was written to GCF_014490445.1_ASM1449044v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:02,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:02,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:02,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/checkm_data
[2024-01-24 13:19:02,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:02,587] [INFO] Task started: CheckM
[2024-01-24 13:19:02,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490445.1_ASM1449044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490445.1_ASM1449044v1_genomic.fna/checkm_input GCF_014490445.1_ASM1449044v1_genomic.fna/checkm_result
[2024-01-24 13:19:54,365] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:54,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:54,392] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:54,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:54,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490445.1_ASM1449044v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:54,393] [INFO] Task started: Blastn
[2024-01-24 13:19:54,394] [INFO] Running command: blastn -query GCF_014490445.1_ASM1449044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb907f5bb-6a9e-4694-a8a4-2f4399f42035/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490445.1_ASM1449044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:56,207] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:56,211] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:56,211] [INFO] Target genome list was writen to GCF_014490445.1_ASM1449044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:56,228] [INFO] Task started: fastANI
[2024-01-24 13:19:56,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg96336e0b-bc3d-4da6-b5e0-596c3e20b6c1/GCF_014490445.1_ASM1449044v1_genomic.fna.gz --refList GCF_014490445.1_ASM1449044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490445.1_ASM1449044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:05,877] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:05,884] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:05,884] [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_014490445.1	s__Roseomonas ludipueritiae	100.0	1578	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003696345.1	s__Roseomonas sp003696345	91.554	1284	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017654485.1	s__Roseomonas sp017654485	85.9541	1012	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.93	99.93	0.97	0.97	2	-
GCF_017355405.1	s__Roseomonas sp017355405	83.5005	944	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014490485.1	s__Roseomonas aerophila	83.391	965	1593	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	82.7265	861	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386565.1	s__Roseomonas oryzae	81.7107	825	1593	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 13:20:05,886] [INFO] GTDB search result was written to GCF_014490445.1_ASM1449044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:05,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:05,889] [INFO] DFAST_QC result json was written to GCF_014490445.1_ASM1449044v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:05,890] [INFO] DFAST_QC completed!
[2024-01-24 13:20:05,890] [INFO] Total running time: 0h1m34s