[2024-01-24 13:55:41,136] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:41,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:41,139] [INFO] DQC Reference Directory: /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference
[2024-01-24 13:55:42,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,572] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,572] [INFO] Running command: gunzip -c /var/lib/cwl/stgc552d575-f1b5-4337-bfac-1dd3ac74f2c3/GCF_014490485.1_ASM1449048v1_genomic.fna.gz | prodigal -d GCF_014490485.1_ASM1449048v1_genomic.fna/cds.fna -a GCF_014490485.1_ASM1449048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:00,507] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:00,507] [INFO] Task started: HMMsearch
[2024-01-24 13:56:00,507] [INFO] Running command: hmmsearch --tblout GCF_014490485.1_ASM1449048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/reference_markers.hmm GCF_014490485.1_ASM1449048v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:00,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:00,822] [INFO] Found 6/6 markers.
[2024-01-24 13:56:00,873] [INFO] Query marker FASTA was written to GCF_014490485.1_ASM1449048v1_genomic.fna/markers.fasta
[2024-01-24 13:56:00,873] [INFO] Task started: Blastn
[2024-01-24 13:56:00,873] [INFO] Running command: blastn -query GCF_014490485.1_ASM1449048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/reference_markers.fasta -out GCF_014490485.1_ASM1449048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:01,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:01,927] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:01,928] [INFO] Target genome list was writen to GCF_014490485.1_ASM1449048v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:01,934] [INFO] Task started: fastANI
[2024-01-24 13:56:01,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgc552d575-f1b5-4337-bfac-1dd3ac74f2c3/GCF_014490485.1_ASM1449048v1_genomic.fna.gz --refList GCF_014490485.1_ASM1449048v1_genomic.fna/target_genomes.txt --output GCF_014490485.1_ASM1449048v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:14,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:14,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:14,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:14,027] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:14,027] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:14,027] [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 aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	100.0	1810	1817	95	conclusive
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	83.3487	951	1817	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	83.3485	1094	1817	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	82.8576	1025	1817	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	82.8516	971	1817	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	81.5357	877	1817	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.4058	605	1817	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.3736	483	1817	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.0608	551	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:14,029] [INFO] DFAST Taxonomy check result was written to GCF_014490485.1_ASM1449048v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:14,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:14,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:14,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/checkm_data
[2024-01-24 13:56:14,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:14,094] [INFO] Task started: CheckM
[2024-01-24 13:56:14,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490485.1_ASM1449048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490485.1_ASM1449048v1_genomic.fna/checkm_input GCF_014490485.1_ASM1449048v1_genomic.fna/checkm_result
[2024-01-24 13:57:04,635] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490485.1_ASM1449048v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,660] [INFO] Task started: Blastn
[2024-01-24 13:57:04,660] [INFO] Running command: blastn -query GCF_014490485.1_ASM1449048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge762619d-ea79-4b40-b926-1ffe252bcf43/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490485.1_ASM1449048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,528] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:06,528] [INFO] Target genome list was writen to GCF_014490485.1_ASM1449048v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:06,539] [INFO] Task started: fastANI
[2024-01-24 13:57:06,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgc552d575-f1b5-4337-bfac-1dd3ac74f2c3/GCF_014490485.1_ASM1449048v1_genomic.fna.gz --refList GCF_014490485.1_ASM1449048v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490485.1_ASM1449048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:15,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:15,807] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:15,807] [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_014490485.1	s__Roseomonas aerophila	100.0	1810	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000245075.1	s__Roseomonas sp000245075	84.0653	1100	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	83.3862	1088	1817	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	83.3638	950	1817	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	82.8603	970	1817	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	82.8384	1027	1817	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:15,809] [INFO] GTDB search result was written to GCF_014490485.1_ASM1449048v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:15,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:15,813] [INFO] DFAST_QC result json was written to GCF_014490485.1_ASM1449048v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:15,813] [INFO] DFAST_QC completed!
[2024-01-24 13:57:15,813] [INFO] Total running time: 0h1m35s