[2024-01-24 13:49:30,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,584] [INFO] DQC Reference Directory: /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference
[2024-01-24 13:49:31,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,901] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,901] [INFO] Running command: gunzip -c /var/lib/cwl/stga370c29a-1667-4487-8a30-0d98a8238ac0/GCF_005048855.1_ASM504885v1_genomic.fna.gz | prodigal -d GCF_005048855.1_ASM504885v1_genomic.fna/cds.fna -a GCF_005048855.1_ASM504885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,528] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,529] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,529] [INFO] Running command: hmmsearch --tblout GCF_005048855.1_ASM504885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/reference_markers.hmm GCF_005048855.1_ASM504885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:55,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:55,953] [INFO] Found 6/6 markers.
[2024-01-24 13:49:55,999] [INFO] Query marker FASTA was written to GCF_005048855.1_ASM504885v1_genomic.fna/markers.fasta
[2024-01-24 13:49:56,000] [INFO] Task started: Blastn
[2024-01-24 13:49:56,000] [INFO] Running command: blastn -query GCF_005048855.1_ASM504885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/reference_markers.fasta -out GCF_005048855.1_ASM504885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,650] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,654] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:56,654] [INFO] Target genome list was writen to GCF_005048855.1_ASM504885v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:56,659] [INFO] Task started: fastANI
[2024-01-24 13:49:56,659] [INFO] Running command: fastANI --query /var/lib/cwl/stga370c29a-1667-4487-8a30-0d98a8238ac0/GCF_005048855.1_ASM504885v1_genomic.fna.gz --refList GCF_005048855.1_ASM504885v1_genomic.fna/target_genomes.txt --output GCF_005048855.1_ASM504885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:07,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:07,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:07,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:07,052] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:07,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:07,053] [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
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	100.0	1787	1787	95	conclusive
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	88.8034	746	1787	95	below_threshold
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	87.4581	1213	1787	95	below_threshold
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	87.4265	1214	1787	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	78.4607	179	1787	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.2227	189	1787	95	below_threshold
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	78.1007	187	1787	95	below_threshold
Sphingobacterium griseoflavum	strain=CGMCC 1.12966	GCA_014653155.1	1474952	1474952	type	True	78.0243	123	1787	95	below_threshold
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	77.9045	164	1787	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	77.8714	184	1787	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.821	144	1787	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.793	53	1787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:07,054] [INFO] DFAST Taxonomy check result was written to GCF_005048855.1_ASM504885v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:07,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:07,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:07,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/checkm_data
[2024-01-24 13:50:07,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:07,110] [INFO] Task started: CheckM
[2024-01-24 13:50:07,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005048855.1_ASM504885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005048855.1_ASM504885v1_genomic.fna/checkm_input GCF_005048855.1_ASM504885v1_genomic.fna/checkm_result
[2024-01-24 13:51:12,966] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:12,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:12,987] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:12,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:12,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005048855.1_ASM504885v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:12,988] [INFO] Task started: Blastn
[2024-01-24 13:51:12,989] [INFO] Running command: blastn -query GCF_005048855.1_ASM504885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge301ed9d-c152-4992-88b2-8c848f1e62a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_005048855.1_ASM504885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:13,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:13,745] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:13,745] [INFO] Target genome list was writen to GCF_005048855.1_ASM504885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:13,778] [INFO] Task started: fastANI
[2024-01-24 13:51:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stga370c29a-1667-4487-8a30-0d98a8238ac0/GCF_005048855.1_ASM504885v1_genomic.fna.gz --refList GCF_005048855.1_ASM504885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005048855.1_ASM504885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:23,271] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:23,285] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:23,286] [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_005048855.1	s__Sphingobacterium olei	100.0	1787	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006476045.1	s__Sphingobacterium lumbrici	88.8221	745	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005049105.1	s__Sphingobacterium alkalisoli	87.4351	1213	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015209965.1	s__Sphingobacterium sp015209965	86.4882	1162	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	78.23	188	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	78.2199	181	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.1549	147	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCF_008520265.1	s__Sphingobacterium cavernae	78.1325	187	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	78.0559	164	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363245.1	s__Sphingobacterium yanglingense	78.0349	180	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	77.976	161	1787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:23,287] [INFO] GTDB search result was written to GCF_005048855.1_ASM504885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:23,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:23,291] [INFO] DFAST_QC result json was written to GCF_005048855.1_ASM504885v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:23,291] [INFO] DFAST_QC completed!
[2024-01-24 13:51:23,291] [INFO] Total running time: 0h1m53s