[2024-01-24 13:12:52,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference
[2024-01-24 13:12:53,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,488] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3c6f805-5ea1-42b8-9f65-4e7e9918a7c3/GCF_007971525.1_ASM797152v1_genomic.fna.gz | prodigal -d GCF_007971525.1_ASM797152v1_genomic.fna/cds.fna -a GCF_007971525.1_ASM797152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:28,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:28,966] [INFO] Task started: HMMsearch
[2024-01-24 13:13:28,966] [INFO] Running command: hmmsearch --tblout GCF_007971525.1_ASM797152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/reference_markers.hmm GCF_007971525.1_ASM797152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:29,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:29,373] [INFO] Found 6/6 markers.
[2024-01-24 13:13:29,432] [INFO] Query marker FASTA was written to GCF_007971525.1_ASM797152v1_genomic.fna/markers.fasta
[2024-01-24 13:13:29,433] [INFO] Task started: Blastn
[2024-01-24 13:13:29,433] [INFO] Running command: blastn -query GCF_007971525.1_ASM797152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/reference_markers.fasta -out GCF_007971525.1_ASM797152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:30,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:30,095] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:30,096] [INFO] Target genome list was writen to GCF_007971525.1_ASM797152v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:30,111] [INFO] Task started: fastANI
[2024-01-24 13:13:30,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3c6f805-5ea1-42b8-9f65-4e7e9918a7c3/GCF_007971525.1_ASM797152v1_genomic.fna.gz --refList GCF_007971525.1_ASM797152v1_genomic.fna/target_genomes.txt --output GCF_007971525.1_ASM797152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:52,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:52,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:52,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:52,118] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:52,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:52,119] [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 ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	100.0	2601	2603	95	conclusive
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	79.9283	893	2603	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	79.059	757	2603	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	79.0357	762	2603	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	79.0078	767	2603	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	78.7175	839	2603	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	78.6107	776	2603	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	78.4478	704	2603	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.9181	468	2603	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.7473	451	2603	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.7431	393	2603	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.6426	369	2603	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.6043	319	2603	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.5574	473	2603	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.5468	457	2603	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.5306	253	2603	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.5232	284	2603	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.4779	395	2603	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	77.2035	183	2603	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:52,122] [INFO] DFAST Taxonomy check result was written to GCF_007971525.1_ASM797152v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:52,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:52,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:52,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/checkm_data
[2024-01-24 13:13:52,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:52,199] [INFO] Task started: CheckM
[2024-01-24 13:13:52,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007971525.1_ASM797152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007971525.1_ASM797152v1_genomic.fna/checkm_input GCF_007971525.1_ASM797152v1_genomic.fna/checkm_result
[2024-01-24 13:15:20,898] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:20,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:20,924] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:20,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:20,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007971525.1_ASM797152v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:20,925] [INFO] Task started: Blastn
[2024-01-24 13:15:20,925] [INFO] Running command: blastn -query GCF_007971525.1_ASM797152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c805e24-8b44-43fd-afd3-fdd066a39936/dqc_reference/reference_markers_gtdb.fasta -out GCF_007971525.1_ASM797152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:21,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:21,777] [INFO] Selected 12 target genomes.
[2024-01-24 13:15:21,777] [INFO] Target genome list was writen to GCF_007971525.1_ASM797152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:21,788] [INFO] Task started: fastANI
[2024-01-24 13:15:21,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3c6f805-5ea1-42b8-9f65-4e7e9918a7c3/GCF_007971525.1_ASM797152v1_genomic.fna.gz --refList GCF_007971525.1_ASM797152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007971525.1_ASM797152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:39,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:39,502] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:39,502] [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_007971525.1	s__Mucilaginibacter ginsenosidivorax	100.0	2600	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110415.1	s__Mucilaginibacter sp900110415	89.1358	1844	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	81.6859	1330	2603	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	79.937	892	2603	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	79.2885	818	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	79.166	780	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089895.1	s__Mucilaginibacter inviolabilis	79.0444	760	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	78.6814	840	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	78.5733	872	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148845.1	s__Mucilaginibacter oryzae	78.4449	705	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	77.7041	171	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	77.3309	286	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:39,510] [INFO] GTDB search result was written to GCF_007971525.1_ASM797152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:39,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:39,521] [INFO] DFAST_QC result json was written to GCF_007971525.1_ASM797152v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:39,521] [INFO] DFAST_QC completed!
[2024-01-24 13:15:39,521] [INFO] Total running time: 0h2m47s