[2024-01-24 11:43:41,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference
[2024-01-24 11:43:43,445] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,446] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,446] [INFO] Running command: gunzip -c /var/lib/cwl/stgba652faf-8662-466b-9de7-c0517ffe472e/GCF_006476045.1_ASM647604v1_genomic.fna.gz | prodigal -d GCF_006476045.1_ASM647604v1_genomic.fna/cds.fna -a GCF_006476045.1_ASM647604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:56,487] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:56,488] [INFO] Task started: HMMsearch
[2024-01-24 11:43:56,488] [INFO] Running command: hmmsearch --tblout GCF_006476045.1_ASM647604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/reference_markers.hmm GCF_006476045.1_ASM647604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:56,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:56,842] [INFO] Found 6/6 markers.
[2024-01-24 11:43:56,879] [INFO] Query marker FASTA was written to GCF_006476045.1_ASM647604v1_genomic.fna/markers.fasta
[2024-01-24 11:43:56,880] [INFO] Task started: Blastn
[2024-01-24 11:43:56,880] [INFO] Running command: blastn -query GCF_006476045.1_ASM647604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/reference_markers.fasta -out GCF_006476045.1_ASM647604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:57,508] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:57,512] [INFO] Selected 10 target genomes.
[2024-01-24 11:43:57,512] [INFO] Target genome list was writen to GCF_006476045.1_ASM647604v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:57,516] [INFO] Task started: fastANI
[2024-01-24 11:43:57,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgba652faf-8662-466b-9de7-c0517ffe472e/GCF_006476045.1_ASM647604v1_genomic.fna.gz --refList GCF_006476045.1_ASM647604v1_genomic.fna/target_genomes.txt --output GCF_006476045.1_ASM647604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:06,288] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:06,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:06,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:06,298] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:06,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:06,299] [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 lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	100.0	1030	1031	95	conclusive
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	88.8042	752	1031	95	below_threshold
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	83.4419	668	1031	95	below_threshold
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	83.3301	687	1031	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	78.3399	178	1031	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.2953	180	1031	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	78.2163	191	1031	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	78.1305	128	1031	95	below_threshold
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	77.906	152	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:06,307] [INFO] DFAST Taxonomy check result was written to GCF_006476045.1_ASM647604v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:06,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:06,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:06,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/checkm_data
[2024-01-24 11:44:06,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:06,355] [INFO] Task started: CheckM
[2024-01-24 11:44:06,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006476045.1_ASM647604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006476045.1_ASM647604v1_genomic.fna/checkm_input GCF_006476045.1_ASM647604v1_genomic.fna/checkm_result
[2024-01-24 11:44:47,991] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:47,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:48,013] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:48,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:48,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006476045.1_ASM647604v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:48,015] [INFO] Task started: Blastn
[2024-01-24 11:44:48,015] [INFO] Running command: blastn -query GCF_006476045.1_ASM647604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg382c2dd5-e66b-413c-9c44-e6b905abdf5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_006476045.1_ASM647604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:48,800] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:48,804] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:48,804] [INFO] Target genome list was writen to GCF_006476045.1_ASM647604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:48,820] [INFO] Task started: fastANI
[2024-01-24 11:44:48,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgba652faf-8662-466b-9de7-c0517ffe472e/GCF_006476045.1_ASM647604v1_genomic.fna.gz --refList GCF_006476045.1_ASM647604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006476045.1_ASM647604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:58,291] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:58,306] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:58,306] [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_006476045.1	s__Sphingobacterium lumbrici	100.0	1030	1031	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_005048855.1	s__Sphingobacterium olei	88.8233	751	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209965.1	s__Sphingobacterium sp015209965	85.6281	687	1031	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	83.3077	689	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011043515.1	s__Sphingobacterium sp011043515	78.7894	166	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_009829075.1	s__Sphingobacterium composti	78.3364	178	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342685.1	s__Sphingobacterium alimentarium	78.3253	180	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901472535.1	s__Sphingobacterium daejeonense	78.3199	139	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.25	97.25	0.90	0.90	2	-
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	78.2638	188	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_900187125.1	s__Sphingobacterium mizutaii	78.2073	133	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCA_000938735.2	s__Sphingobacterium sp000938735	78.0024	132	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.17	98.17	0.81	0.81	2	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	77.906	152	1031	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 11:44:58,309] [INFO] GTDB search result was written to GCF_006476045.1_ASM647604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:58,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:58,314] [INFO] DFAST_QC result json was written to GCF_006476045.1_ASM647604v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:58,314] [INFO] DFAST_QC completed!
[2024-01-24 11:44:58,315] [INFO] Total running time: 0h1m16s