[2024-01-24 13:32:35,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,008] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference
[2024-01-24 13:32:36,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,341] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,342] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77b73fd-38ef-4585-a1ab-a971e1060e2e/GCF_011392115.1_ASM1139211v1_genomic.fna.gz | prodigal -d GCF_011392115.1_ASM1139211v1_genomic.fna/cds.fna -a GCF_011392115.1_ASM1139211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,989] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,990] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,990] [INFO] Running command: hmmsearch --tblout GCF_011392115.1_ASM1139211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/reference_markers.hmm GCF_011392115.1_ASM1139211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:46,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:46,336] [INFO] Found 6/6 markers.
[2024-01-24 13:32:46,365] [INFO] Query marker FASTA was written to GCF_011392115.1_ASM1139211v1_genomic.fna/markers.fasta
[2024-01-24 13:32:46,366] [INFO] Task started: Blastn
[2024-01-24 13:32:46,366] [INFO] Running command: blastn -query GCF_011392115.1_ASM1139211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/reference_markers.fasta -out GCF_011392115.1_ASM1139211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,084] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:47,084] [INFO] Target genome list was writen to GCF_011392115.1_ASM1139211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,089] [INFO] Task started: fastANI
[2024-01-24 13:32:47,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77b73fd-38ef-4585-a1ab-a971e1060e2e/GCF_011392115.1_ASM1139211v1_genomic.fna.gz --refList GCF_011392115.1_ASM1139211v1_genomic.fna/target_genomes.txt --output GCF_011392115.1_ASM1139211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:58,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:58,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:58,317] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:58,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:58,317] [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
Flavobacterium difficile	strain=KDG-16	GCA_011392115.1	2709659	2709659	type	True	100.0	973	975	95	conclusive
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	84.9486	712	975	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	84.3375	691	975	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	81.3118	617	975	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.6101	346	975	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.6064	362	975	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.5928	333	975	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	78.4206	416	975	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	78.2406	282	975	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.1741	279	975	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.9675	268	975	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	77.7722	312	975	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.7573	280	975	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.3701	182	975	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.2717	194	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,319] [INFO] DFAST Taxonomy check result was written to GCF_011392115.1_ASM1139211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:58,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:58,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:58,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/checkm_data
[2024-01-24 13:32:58,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:58,353] [INFO] Task started: CheckM
[2024-01-24 13:32:58,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011392115.1_ASM1139211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011392115.1_ASM1139211v1_genomic.fna/checkm_input GCF_011392115.1_ASM1139211v1_genomic.fna/checkm_result
[2024-01-24 13:33:32,696] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:32,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:32,724] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:32,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:32,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011392115.1_ASM1139211v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:32,726] [INFO] Task started: Blastn
[2024-01-24 13:33:32,726] [INFO] Running command: blastn -query GCF_011392115.1_ASM1139211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd894a5-6107-4a57-8918-24e0f3f3753a/dqc_reference/reference_markers_gtdb.fasta -out GCF_011392115.1_ASM1139211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:33,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:33,770] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:33,770] [INFO] Target genome list was writen to GCF_011392115.1_ASM1139211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:33,786] [INFO] Task started: fastANI
[2024-01-24 13:33:33,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77b73fd-38ef-4585-a1ab-a971e1060e2e/GCF_011392115.1_ASM1139211v1_genomic.fna.gz --refList GCF_011392115.1_ASM1139211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011392115.1_ASM1139211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:39,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:39,188] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:39,188] [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_011392115.1	s__Flavobacterium sp011392115	100.0	973	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011305415.1	s__Flavobacterium bernardetii	84.9488	712	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900108955.1	s__Flavobacterium terrigena	84.3271	692	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800945.1	s__Flavobacterium sp001800945	84.0282	447	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985075.1	s__Flavobacterium sp017985075	82.2178	506	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293045.1	s__Flavobacterium sp004293045	82.0749	412	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110615.1	s__Flavobacterium urocaniciphilum	81.3118	617	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	77.6461	277	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,190] [INFO] GTDB search result was written to GCF_011392115.1_ASM1139211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:39,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:39,194] [INFO] DFAST_QC result json was written to GCF_011392115.1_ASM1139211v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:39,194] [INFO] DFAST_QC completed!
[2024-01-24 13:33:39,194] [INFO] Total running time: 0h1m4s