[2024-01-25 17:36:35,637] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:35,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:35,639] [INFO] DQC Reference Directory: /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference
[2024-01-25 17:36:36,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:36,760] [INFO] Task started: Prodigal
[2024-01-25 17:36:36,760] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbd11101-940b-4a85-bdb9-e1ba709179aa/GCF_028596025.1_ASM2859602v1_genomic.fna.gz | prodigal -d GCF_028596025.1_ASM2859602v1_genomic.fna/cds.fna -a GCF_028596025.1_ASM2859602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:58,207] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:58,208] [INFO] Task started: HMMsearch
[2024-01-25 17:36:58,208] [INFO] Running command: hmmsearch --tblout GCF_028596025.1_ASM2859602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/reference_markers.hmm GCF_028596025.1_ASM2859602v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:58,486] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:58,487] [INFO] Found 6/6 markers.
[2024-01-25 17:36:58,534] [INFO] Query marker FASTA was written to GCF_028596025.1_ASM2859602v1_genomic.fna/markers.fasta
[2024-01-25 17:36:58,534] [INFO] Task started: Blastn
[2024-01-25 17:36:58,534] [INFO] Running command: blastn -query GCF_028596025.1_ASM2859602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/reference_markers.fasta -out GCF_028596025.1_ASM2859602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:59,131] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:59,134] [INFO] Selected 15 target genomes.
[2024-01-25 17:36:59,134] [INFO] Target genome list was writen to GCF_028596025.1_ASM2859602v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:59,138] [INFO] Task started: fastANI
[2024-01-25 17:36:59,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbd11101-940b-4a85-bdb9-e1ba709179aa/GCF_028596025.1_ASM2859602v1_genomic.fna.gz --refList GCF_028596025.1_ASM2859602v1_genomic.fna/target_genomes.txt --output GCF_028596025.1_ASM2859602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:14,877] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:14,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:14,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:14,887] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:37:14,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:37:14,888] [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
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	82.5361	1081	2052	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	82.5361	1056	2052	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	81.256	904	2052	95	below_threshold
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	78.0694	221	2052	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.9718	357	2052	95	below_threshold
Mucilaginibacter ginkgonis	strain=HMF7856	GCA_009754905.2	2682091	2682091	type	True	77.7574	294	2052	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.7454	312	2052	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.716	362	2052	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.5049	369	2052	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.4766	330	2052	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.4169	348	2052	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.3634	262	2052	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3369	305	2052	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.3056	318	2052	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.2976	267	2052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:14,889] [INFO] DFAST Taxonomy check result was written to GCF_028596025.1_ASM2859602v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:14,889] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:14,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:14,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/checkm_data
[2024-01-25 17:37:14,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:14,947] [INFO] Task started: CheckM
[2024-01-25 17:37:14,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028596025.1_ASM2859602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028596025.1_ASM2859602v1_genomic.fna/checkm_input GCF_028596025.1_ASM2859602v1_genomic.fna/checkm_result
[2024-01-25 17:38:12,858] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:12,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:12,893] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:12,893] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:12,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028596025.1_ASM2859602v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:12,895] [INFO] Task started: Blastn
[2024-01-25 17:38:12,895] [INFO] Running command: blastn -query GCF_028596025.1_ASM2859602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge088dccc-9f4a-4e40-ad8d-afa00e0ec6b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_028596025.1_ASM2859602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:13,819] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:13,823] [INFO] Selected 16 target genomes.
[2024-01-25 17:38:13,823] [INFO] Target genome list was writen to GCF_028596025.1_ASM2859602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:13,829] [INFO] Task started: fastANI
[2024-01-25 17:38:13,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbd11101-940b-4a85-bdb9-e1ba709179aa/GCF_028596025.1_ASM2859602v1_genomic.fna.gz --refList GCF_028596025.1_ASM2859602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028596025.1_ASM2859602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:30,181] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:30,191] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:38:30,191] [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
GCA_903644075.1	s__Mucilaginibacter sp903644075	86.6153	1146	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	82.5346	1081	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009928685.1	s__Mucilaginibacter sp009928685	81.2488	906	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755275.1	s__Mucilaginibacter aquatilis	78.0887	221	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754905.2	s__Mucilaginibacter ginkgonis	77.7732	292	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635825.1	s__Mucilaginibacter galii	77.7661	310	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432115.1	s__Mucilaginibacter sp003432115	77.7226	362	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	77.6673	314	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390515.1	s__Mucilaginibacter sp018390515	77.5879	300	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.5049	369	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	77.4882	366	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	77.4838	262	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	77.4454	355	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	77.4252	292	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.3843	260	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	77.0085	281	2052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:30,192] [INFO] GTDB search result was written to GCF_028596025.1_ASM2859602v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:30,193] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:30,196] [INFO] DFAST_QC result json was written to GCF_028596025.1_ASM2859602v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:30,196] [INFO] DFAST_QC completed!
[2024-01-25 17:38:30,196] [INFO] Total running time: 0h1m55s