[2024-01-24 12:53:56,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference
[2024-01-24 12:53:58,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,060] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,061] [INFO] Running command: gunzip -c /var/lib/cwl/stga517c495-b71c-4b22-9fa8-3609e6357499/GCF_000017565.1_ASM1756v1_genomic.fna.gz | prodigal -d GCF_000017565.1_ASM1756v1_genomic.fna/cds.fna -a GCF_000017565.1_ASM1756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:10,170] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:10,170] [INFO] Task started: HMMsearch
[2024-01-24 12:54:10,171] [INFO] Running command: hmmsearch --tblout GCF_000017565.1_ASM1756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/reference_markers.hmm GCF_000017565.1_ASM1756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:10,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:10,439] [INFO] Found 6/6 markers.
[2024-01-24 12:54:10,471] [INFO] Query marker FASTA was written to GCF_000017565.1_ASM1756v1_genomic.fna/markers.fasta
[2024-01-24 12:54:10,471] [INFO] Task started: Blastn
[2024-01-24 12:54:10,471] [INFO] Running command: blastn -query GCF_000017565.1_ASM1756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/reference_markers.fasta -out GCF_000017565.1_ASM1756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:11,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:11,472] [INFO] Selected 23 target genomes.
[2024-01-24 12:54:11,473] [INFO] Target genome list was writen to GCF_000017565.1_ASM1756v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:11,481] [INFO] Task started: fastANI
[2024-01-24 12:54:11,481] [INFO] Running command: fastANI --query /var/lib/cwl/stga517c495-b71c-4b22-9fa8-3609e6357499/GCF_000017565.1_ASM1756v1_genomic.fna.gz --refList GCF_000017565.1_ASM1756v1_genomic.fna/target_genomes.txt --output GCF_000017565.1_ASM1756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:30,010] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:30,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:30,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:30,028] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:30,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:30,029] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	100.0	1294	1304	95	conclusive
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.976	508	1304	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.3657	538	1304	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.9228	319	1304	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.0234	202	1304	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.9275	190	1304	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.8812	174	1304	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.8442	177	1304	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	76.8383	180	1304	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.7903	167	1304	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.7893	150	1304	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.7751	167	1304	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.7718	122	1304	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	76.7327	110	1304	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	76.6563	156	1304	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.6194	156	1304	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	76.4799	195	1304	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.436	165	1304	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.2637	177	1304	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.1892	102	1304	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.132	131	1304	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	76.0462	71	1304	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	75.9378	88	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,030] [INFO] DFAST Taxonomy check result was written to GCF_000017565.1_ASM1756v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:30,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:30,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:30,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/checkm_data
[2024-01-24 12:54:30,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:30,073] [INFO] Task started: CheckM
[2024-01-24 12:54:30,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017565.1_ASM1756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017565.1_ASM1756v1_genomic.fna/checkm_input GCF_000017565.1_ASM1756v1_genomic.fna/checkm_result
[2024-01-24 12:55:05,765] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:05,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:05,783] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:05,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:05,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017565.1_ASM1756v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:05,784] [INFO] Task started: Blastn
[2024-01-24 12:55:05,784] [INFO] Running command: blastn -query GCF_000017565.1_ASM1756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f26389-f715-4787-ad3e-8fd0c7f4443f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017565.1_ASM1756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:07,611] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:07,614] [INFO] Selected 10 target genomes.
[2024-01-24 12:55:07,614] [INFO] Target genome list was writen to GCF_000017565.1_ASM1756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:07,621] [INFO] Task started: fastANI
[2024-01-24 12:55:07,621] [INFO] Running command: fastANI --query /var/lib/cwl/stga517c495-b71c-4b22-9fa8-3609e6357499/GCF_000017565.1_ASM1756v1_genomic.fna.gz --refList GCF_000017565.1_ASM1756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017565.1_ASM1756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:15,689] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:15,699] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:15,699] [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_000017565.1	s__Parvibaculum lavamentivorans	100.0	1296	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002842875.1	s__Parvibaculum sp002842875	82.178	697	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	82.1253	810	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_017642695.1	s__Parvibaculum sp017642695	82.0347	794	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002841195.1	s__Parvibaculum sp002841195	82.0204	621	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	81.7013	468	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	81.4692	718	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017643025.1	s__RCIO01 sp017643025	76.9074	139	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339465.1	s__Ancylobacter aquaticus	76.6182	159	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201075.1	s__Lichenicola cladoniae	75.9177	85	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:15,701] [INFO] GTDB search result was written to GCF_000017565.1_ASM1756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:15,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:15,706] [INFO] DFAST_QC result json was written to GCF_000017565.1_ASM1756v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:15,706] [INFO] DFAST_QC completed!
[2024-01-24 12:55:15,706] [INFO] Total running time: 0h1m19s