[2024-01-24 10:49:34,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference
[2024-01-24 10:49:35,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,714] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2624836-1321-4813-997b-caa8dcb8fa60/GCF_001697225.1_ASM169722v1_genomic.fna.gz | prodigal -d GCF_001697225.1_ASM169722v1_genomic.fna/cds.fna -a GCF_001697225.1_ASM169722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:46,000] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:46,000] [INFO] Task started: HMMsearch
[2024-01-24 10:49:46,000] [INFO] Running command: hmmsearch --tblout GCF_001697225.1_ASM169722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/reference_markers.hmm GCF_001697225.1_ASM169722v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:46,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:46,285] [INFO] Found 6/6 markers.
[2024-01-24 10:49:46,314] [INFO] Query marker FASTA was written to GCF_001697225.1_ASM169722v1_genomic.fna/markers.fasta
[2024-01-24 10:49:46,314] [INFO] Task started: Blastn
[2024-01-24 10:49:46,314] [INFO] Running command: blastn -query GCF_001697225.1_ASM169722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/reference_markers.fasta -out GCF_001697225.1_ASM169722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:47,233] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:47,237] [INFO] Selected 28 target genomes.
[2024-01-24 10:49:47,237] [INFO] Target genome list was writen to GCF_001697225.1_ASM169722v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:47,248] [INFO] Task started: fastANI
[2024-01-24 10:49:47,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2624836-1321-4813-997b-caa8dcb8fa60/GCF_001697225.1_ASM169722v1_genomic.fna.gz --refList GCF_001697225.1_ASM169722v1_genomic.fna/target_genomes.txt --output GCF_001697225.1_ASM169722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:05,609] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:05,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:05,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:05,635] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:05,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:05,636] [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
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	100.0	1081	1081	95	conclusive
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	77.1476	208	1081	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.9893	187	1081	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.9693	293	1081	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.9684	213	1081	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.9358	120	1081	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.8796	181	1081	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.8645	201	1081	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.853	133	1081	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.7722	131	1081	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	76.7649	163	1081	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.73	243	1081	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.7261	208	1081	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.7152	198	1081	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.6586	128	1081	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.6524	191	1081	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6293	224	1081	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.5821	213	1081	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.5644	231	1081	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.5125	176	1081	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	76.4937	233	1081	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.48	98	1081	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.4762	205	1081	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.4099	205	1081	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.3651	237	1081	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	76.3483	133	1081	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	76.2357	158	1081	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.1434	208	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:05,638] [INFO] DFAST Taxonomy check result was written to GCF_001697225.1_ASM169722v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:05,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:05,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:05,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/checkm_data
[2024-01-24 10:50:05,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:05,672] [INFO] Task started: CheckM
[2024-01-24 10:50:05,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001697225.1_ASM169722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001697225.1_ASM169722v1_genomic.fna/checkm_input GCF_001697225.1_ASM169722v1_genomic.fna/checkm_result
[2024-01-24 10:50:44,468] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:44,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:44,492] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:44,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:44,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001697225.1_ASM169722v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:44,493] [INFO] Task started: Blastn
[2024-01-24 10:50:44,493] [INFO] Running command: blastn -query GCF_001697225.1_ASM169722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87e8eb19-2e6c-4fa7-9f84-4f20dfad9217/dqc_reference/reference_markers_gtdb.fasta -out GCF_001697225.1_ASM169722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:46,220] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:46,226] [INFO] Selected 16 target genomes.
[2024-01-24 10:50:46,226] [INFO] Target genome list was writen to GCF_001697225.1_ASM169722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:46,239] [INFO] Task started: fastANI
[2024-01-24 10:50:46,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2624836-1321-4813-997b-caa8dcb8fa60/GCF_001697225.1_ASM169722v1_genomic.fna.gz --refList GCF_001697225.1_ASM169722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001697225.1_ASM169722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:57,361] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:57,375] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:57,375] [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_001697225.1	s__Immundisolibacter cernigliae	100.0	1081	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014359565.1	s__Immundisolibacter sp014359565	93.8383	875	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526065.1	s__Immundisolibacter sp003526065	83.2417	464	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.2286	192	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	77.1656	207	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.068	194	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.9768	294	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001753165.1	s__Acidihalobacter aeolianus	76.9358	120	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	76.8633	263	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429065.1	s__Silanimonas lenta	76.8455	161	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.7595	148	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.7209	241	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_004343305.1	s__Pseudofulvimonas gallinarii	76.6991	155	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.97	99.94	0.98	0.98	3	-
GCF_900115705.1	s__Frateuria_A terrea	76.3829	208	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_008933795.1	s__Contendobacter sp008933795	76.2661	137	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	75.993	111	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:57,377] [INFO] GTDB search result was written to GCF_001697225.1_ASM169722v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:57,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:57,383] [INFO] DFAST_QC result json was written to GCF_001697225.1_ASM169722v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:57,383] [INFO] DFAST_QC completed!
[2024-01-24 10:50:57,383] [INFO] Total running time: 0h1m23s