[2024-01-24 12:44:42,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:42,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:42,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference
[2024-01-24 12:44:43,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,739] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,739] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4a76274-4ed7-4dee-b733-764aea56a413/GCF_009928685.1_ASM992868v1_genomic.fna.gz | prodigal -d GCF_009928685.1_ASM992868v1_genomic.fna/cds.fna -a GCF_009928685.1_ASM992868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:07,179] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:07,180] [INFO] Task started: HMMsearch
[2024-01-24 12:45:07,180] [INFO] Running command: hmmsearch --tblout GCF_009928685.1_ASM992868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/reference_markers.hmm GCF_009928685.1_ASM992868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:07,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:07,526] [INFO] Found 6/6 markers.
[2024-01-24 12:45:07,584] [INFO] Query marker FASTA was written to GCF_009928685.1_ASM992868v1_genomic.fna/markers.fasta
[2024-01-24 12:45:07,585] [INFO] Task started: Blastn
[2024-01-24 12:45:07,585] [INFO] Running command: blastn -query GCF_009928685.1_ASM992868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/reference_markers.fasta -out GCF_009928685.1_ASM992868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:08,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:08,261] [INFO] Selected 16 target genomes.
[2024-01-24 12:45:08,262] [INFO] Target genome list was writen to GCF_009928685.1_ASM992868v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:08,267] [INFO] Task started: fastANI
[2024-01-24 12:45:08,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a76274-4ed7-4dee-b733-764aea56a413/GCF_009928685.1_ASM992868v1_genomic.fna.gz --refList GCF_009928685.1_ASM992868v1_genomic.fna/target_genomes.txt --output GCF_009928685.1_ASM992868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:24,338] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:24,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:24,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:24,352] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:24,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:24,352] [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 agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	100.0	1852	1855	95	conclusive
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	80.6462	836	1855	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	80.6365	820	1855	95	below_threshold
Mucilaginibacter ginkgonis	strain=HMF7856	GCA_009754905.2	2682091	2682091	type	True	79.4454	259	1855	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.8157	297	1855	95	below_threshold
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	77.8134	215	1855	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.6786	297	1855	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.5618	220	1855	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.4678	228	1855	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.3365	196	1855	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.3309	286	1855	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.3161	299	1855	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.2964	331	1855	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.2096	292	1855	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.2069	221	1855	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.1423	270	1855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:24,354] [INFO] DFAST Taxonomy check result was written to GCF_009928685.1_ASM992868v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:24,354] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:24,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:24,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/checkm_data
[2024-01-24 12:45:24,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:24,409] [INFO] Task started: CheckM
[2024-01-24 12:45:24,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009928685.1_ASM992868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009928685.1_ASM992868v1_genomic.fna/checkm_input GCF_009928685.1_ASM992868v1_genomic.fna/checkm_result
[2024-01-24 12:46:28,493] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:28,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:28,522] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:28,522] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:28,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009928685.1_ASM992868v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:28,523] [INFO] Task started: Blastn
[2024-01-24 12:46:28,523] [INFO] Running command: blastn -query GCF_009928685.1_ASM992868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79441e64-29c5-4518-8d98-4d2f6a91671b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009928685.1_ASM992868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:29,340] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:29,344] [INFO] Selected 17 target genomes.
[2024-01-24 12:46:29,344] [INFO] Target genome list was writen to GCF_009928685.1_ASM992868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:29,373] [INFO] Task started: fastANI
[2024-01-24 12:46:29,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a76274-4ed7-4dee-b733-764aea56a413/GCF_009928685.1_ASM992868v1_genomic.fna.gz --refList GCF_009928685.1_ASM992868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009928685.1_ASM992868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:45,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:45,382] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:45,382] [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_009928685.1	s__Mucilaginibacter sp009928685	100.0	1852	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903644075.1	s__Mucilaginibacter sp903644075	80.9243	728	1855	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	80.6534	835	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009754905.2	s__Mucilaginibacter ginkgonis	79.4454	259	1855	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	77.8091	214	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351025.1	s__Mucilaginibacter endophyticus	77.6808	296	1855	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	77.5462	259	1855	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	77.4943	226	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009770985.1	s__Mucilaginibacter sp009770985	77.4405	248	1855	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	77.4049	253	1855	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	77.3208	287	1855	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	77.3145	236	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971525.1	s__Mucilaginibacter ginsenosidivorax	77.3067	300	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	77.2895	247	1855	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	77.2877	332	1855	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	77.2458	236	1855	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	77.2102	291	1855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:45,384] [INFO] GTDB search result was written to GCF_009928685.1_ASM992868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:45,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:45,389] [INFO] DFAST_QC result json was written to GCF_009928685.1_ASM992868v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:45,389] [INFO] DFAST_QC completed!
[2024-01-24 12:46:45,389] [INFO] Total running time: 0h2m3s