[2024-01-24 13:49:33,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference
[2024-01-24 13:49:34,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,828] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg52c6bd8f-79f1-42ed-98bd-e35c2b7e526a/GCF_007990875.1_ASM799087v1_genomic.fna.gz | prodigal -d GCF_007990875.1_ASM799087v1_genomic.fna/cds.fna -a GCF_007990875.1_ASM799087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,483] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,483] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,483] [INFO] Running command: hmmsearch --tblout GCF_007990875.1_ASM799087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/reference_markers.hmm GCF_007990875.1_ASM799087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:55,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:55,879] [INFO] Found 6/6 markers.
[2024-01-24 13:49:55,954] [INFO] Query marker FASTA was written to GCF_007990875.1_ASM799087v1_genomic.fna/markers.fasta
[2024-01-24 13:49:55,954] [INFO] Task started: Blastn
[2024-01-24 13:49:55,954] [INFO] Running command: blastn -query GCF_007990875.1_ASM799087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/reference_markers.fasta -out GCF_007990875.1_ASM799087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,669] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:56,670] [INFO] Target genome list was writen to GCF_007990875.1_ASM799087v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:56,677] [INFO] Task started: fastANI
[2024-01-24 13:49:56,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg52c6bd8f-79f1-42ed-98bd-e35c2b7e526a/GCF_007990875.1_ASM799087v1_genomic.fna.gz --refList GCF_007990875.1_ASM799087v1_genomic.fna/target_genomes.txt --output GCF_007990875.1_ASM799087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:13,043] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:13,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:13,057] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:13,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:13,057] [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 faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	100.0	1737	1738	95	conclusive
Sphingobacterium faecium	strain=DSM 11690	GCA_003054045.1	34087	34087	type	True	99.9992	1738	1738	95	conclusive
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	78.1037	132	1738	95	below_threshold
Sphingobacterium multivorum	strain=FDAARGOS_1203	GCA_016894225.1	28454	28454	type	True	78.0998	248	1738	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	78.0664	251	1738	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	78.0492	172	1738	95	below_threshold
Sphingobacterium multivorum	strain=NCTC11343	GCA_900457465.1	28454	28454	type	True	78.0178	247	1738	95	below_threshold
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	78.0143	162	1738	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	78.0109	235	1738	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.0021	159	1738	95	below_threshold
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	77.8534	255	1738	95	below_threshold
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	77.8368	143	1738	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	77.7984	148	1738	95	below_threshold
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	77.7018	143	1738	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	77.5874	135	1738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,059] [INFO] DFAST Taxonomy check result was written to GCF_007990875.1_ASM799087v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:13,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:13,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:13,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/checkm_data
[2024-01-24 13:50:13,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:13,111] [INFO] Task started: CheckM
[2024-01-24 13:50:13,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990875.1_ASM799087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990875.1_ASM799087v1_genomic.fna/checkm_input GCF_007990875.1_ASM799087v1_genomic.fna/checkm_result
[2024-01-24 13:51:12,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:12,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:12,850] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:12,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:12,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990875.1_ASM799087v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:12,851] [INFO] Task started: Blastn
[2024-01-24 13:51:12,851] [INFO] Running command: blastn -query GCF_007990875.1_ASM799087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a15394d-6789-4d86-a0c2-68bcb07a1504/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990875.1_ASM799087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:13,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:13,684] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:13,684] [INFO] Target genome list was writen to GCF_007990875.1_ASM799087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:13,707] [INFO] Task started: fastANI
[2024-01-24 13:51:13,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg52c6bd8f-79f1-42ed-98bd-e35c2b7e526a/GCF_007990875.1_ASM799087v1_genomic.fna.gz --refList GCF_007990875.1_ASM799087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990875.1_ASM799087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:24,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:24,499] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:24,499] [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_003054045.1	s__Sphingobacterium faecium	99.9992	1738	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.76	97.52	0.94	0.88	3	conclusive
GCA_000938735.2	s__Sphingobacterium sp000938735	92.8979	1322	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.17	98.17	0.81	0.81	2	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	84.0816	1124	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
GCF_000747525.1	s__Sphingobacterium sp000747525	82.0034	831	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017942165.1	s__Sphingobacterium sp017942165	78.5967	170	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933815.1	s__Sphingobacterium sp002933815	78.0744	243	1738	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	77.997	158	1738	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	77.9479	162	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_017834055.1	s__Sphingobacterium sp002429765	77.6425	236	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.80	97.10	0.89	0.87	5	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	77.498	156	1738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCA_002454415.1	s__Sphingobacterium sp002454415	77.488	208	1738	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 13:51:24,501] [INFO] GTDB search result was written to GCF_007990875.1_ASM799087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:24,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:24,506] [INFO] DFAST_QC result json was written to GCF_007990875.1_ASM799087v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:24,506] [INFO] DFAST_QC completed!
[2024-01-24 13:51:24,506] [INFO] Total running time: 0h1m51s