[2024-01-24 13:55:40,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,922] [INFO] DQC Reference Directory: /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference
[2024-01-24 13:55:42,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,191] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7378581-5c50-4f3a-90a3-e8947f764732/GCF_021654335.1_ASM2165433v1_genomic.fna.gz | prodigal -d GCF_021654335.1_ASM2165433v1_genomic.fna/cds.fna -a GCF_021654335.1_ASM2165433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:52,153] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:52,153] [INFO] Task started: HMMsearch
[2024-01-24 13:55:52,153] [INFO] Running command: hmmsearch --tblout GCF_021654335.1_ASM2165433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/reference_markers.hmm GCF_021654335.1_ASM2165433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:52,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:52,429] [INFO] Found 6/6 markers.
[2024-01-24 13:55:52,459] [INFO] Query marker FASTA was written to GCF_021654335.1_ASM2165433v1_genomic.fna/markers.fasta
[2024-01-24 13:55:52,459] [INFO] Task started: Blastn
[2024-01-24 13:55:52,459] [INFO] Running command: blastn -query GCF_021654335.1_ASM2165433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/reference_markers.fasta -out GCF_021654335.1_ASM2165433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:53,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:53,450] [INFO] Selected 28 target genomes.
[2024-01-24 13:55:53,450] [INFO] Target genome list was writen to GCF_021654335.1_ASM2165433v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:53,481] [INFO] Task started: fastANI
[2024-01-24 13:55:53,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7378581-5c50-4f3a-90a3-e8947f764732/GCF_021654335.1_ASM2165433v1_genomic.fna.gz --refList GCF_021654335.1_ASM2165433v1_genomic.fna/target_genomes.txt --output GCF_021654335.1_ASM2165433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:12,272] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:12,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:12,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:12,297] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:12,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:12,297] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	80.8674	416	912	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	78.8181	239	912	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.0401	176	912	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.8708	219	912	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.6359	207	912	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.6062	169	912	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.6016	197	912	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.518	178	912	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	77.4366	173	912	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.4241	151	912	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.408	204	912	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.4015	143	912	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	77.3837	205	912	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	77.2582	179	912	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.2523	135	912	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.1457	138	912	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	77.1328	178	912	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	77.0181	128	912	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.009	168	912	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	76.9822	146	912	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.9547	117	912	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	76.8613	75	912	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.8226	134	912	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	76.7742	141	912	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	76.7046	103	912	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	76.6728	100	912	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	76.6685	170	912	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	76.4497	114	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:12,301] [INFO] DFAST Taxonomy check result was written to GCF_021654335.1_ASM2165433v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:12,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:12,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:12,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/checkm_data
[2024-01-24 13:56:12,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:12,333] [INFO] Task started: CheckM
[2024-01-24 13:56:12,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654335.1_ASM2165433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654335.1_ASM2165433v1_genomic.fna/checkm_input GCF_021654335.1_ASM2165433v1_genomic.fna/checkm_result
[2024-01-24 13:56:45,874] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:45,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:45,896] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:45,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:45,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654335.1_ASM2165433v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:45,898] [INFO] Task started: Blastn
[2024-01-24 13:56:45,898] [INFO] Running command: blastn -query GCF_021654335.1_ASM2165433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga677bd1d-1beb-4ae9-9136-d2ee37f1083e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654335.1_ASM2165433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:47,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:47,734] [INFO] Selected 7 target genomes.
[2024-01-24 13:56:47,734] [INFO] Target genome list was writen to GCF_021654335.1_ASM2165433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:47,751] [INFO] Task started: fastANI
[2024-01-24 13:56:47,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7378581-5c50-4f3a-90a3-e8947f764732/GCF_021654335.1_ASM2165433v1_genomic.fna.gz --refList GCF_021654335.1_ASM2165433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654335.1_ASM2165433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:52,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:52,485] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:56:52,485] [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_000025705.1	s__Sideroxydans lithotrophicus	83.9077	654	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214695.1	s__Sideroxydans sp016214695	83.2301	577	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208015.1	s__Sideroxydans sp016208015	83.0338	566	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	82.9294	561	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445795.1	s__Sideroxydans sp003445795	82.4347	520	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	82.389	548	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_018820925.1	s__Sideroxydans sp018820925	81.8709	561	912	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.99	99.99	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:52,487] [INFO] GTDB search result was written to GCF_021654335.1_ASM2165433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:52,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:52,492] [INFO] DFAST_QC result json was written to GCF_021654335.1_ASM2165433v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:52,493] [INFO] DFAST_QC completed!
[2024-01-24 13:56:52,493] [INFO] Total running time: 0h1m12s