[2024-01-24 15:10:53,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:53,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:53,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference
[2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,634] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4a4d164-f27d-45c5-8504-2bff8c5ae436/GCF_007992375.1_ASM799237v1_genomic.fna.gz | prodigal -d GCF_007992375.1_ASM799237v1_genomic.fna/cds.fna -a GCF_007992375.1_ASM799237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:08,256] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:08,257] [INFO] Task started: HMMsearch
[2024-01-24 15:11:08,257] [INFO] Running command: hmmsearch --tblout GCF_007992375.1_ASM799237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/reference_markers.hmm GCF_007992375.1_ASM799237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:08,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:08,580] [INFO] Found 6/6 markers.
[2024-01-24 15:11:08,613] [INFO] Query marker FASTA was written to GCF_007992375.1_ASM799237v1_genomic.fna/markers.fasta
[2024-01-24 15:11:08,613] [INFO] Task started: Blastn
[2024-01-24 15:11:08,614] [INFO] Running command: blastn -query GCF_007992375.1_ASM799237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/reference_markers.fasta -out GCF_007992375.1_ASM799237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:09,589] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:09,594] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:09,594] [INFO] Target genome list was writen to GCF_007992375.1_ASM799237v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:09,603] [INFO] Task started: fastANI
[2024-01-24 15:11:09,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a4d164-f27d-45c5-8504-2bff8c5ae436/GCF_007992375.1_ASM799237v1_genomic.fna.gz --refList GCF_007992375.1_ASM799237v1_genomic.fna/target_genomes.txt --output GCF_007992375.1_ASM799237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:20,622] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:20,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:20,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:20,635] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:20,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:20,636] [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
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	100.0	1081	1089	95	conclusive
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	99.9998	1088	1089	95	conclusive
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	86.7815	729	1089	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.8715	210	1089	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	77.8424	244	1089	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.6235	145	1089	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	77.602	221	1089	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.0401	145	1089	95	below_threshold
Sulfuriferula thiophila	strain=mst6	GCA_003864975.1	1781211	1781211	type	True	76.9342	182	1089	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.8135	147	1089	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.7052	121	1089	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.3533	107	1089	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	76.283	138	1089	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	75.9116	90	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:20,637] [INFO] DFAST Taxonomy check result was written to GCF_007992375.1_ASM799237v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:20,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:20,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:20,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/checkm_data
[2024-01-24 15:11:20,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:20,682] [INFO] Task started: CheckM
[2024-01-24 15:11:20,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992375.1_ASM799237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992375.1_ASM799237v1_genomic.fna/checkm_input GCF_007992375.1_ASM799237v1_genomic.fna/checkm_result
[2024-01-24 15:11:57,438] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:57,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:57,462] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:57,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:57,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992375.1_ASM799237v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:57,463] [INFO] Task started: Blastn
[2024-01-24 15:11:57,463] [INFO] Running command: blastn -query GCF_007992375.1_ASM799237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0230cb-40d4-45ee-8436-4303f3eca94c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992375.1_ASM799237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:59,219] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:59,224] [INFO] Selected 20 target genomes.
[2024-01-24 15:11:59,224] [INFO] Target genome list was writen to GCF_007992375.1_ASM799237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:59,245] [INFO] Task started: fastANI
[2024-01-24 15:11:59,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a4d164-f27d-45c5-8504-2bff8c5ae436/GCF_007992375.1_ASM799237v1_genomic.fna.gz --refList GCF_007992375.1_ASM799237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992375.1_ASM799237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:10,144] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:10,165] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:10,166] [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_009938015.1	s__Sulfuriferula plumbiphila	99.9998	1088	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003851125.1	s__Sulfuriferula multivorans	86.7821	729	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455595.1	s__Sulfuriferula sp003455595	80.5329	363	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	78.0104	206	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCA_002421825.1	s__UBA6918 sp002421825	77.931	175	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162035.1	s__Sulfuriferula_A sp002162035	77.8958	231	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764585.1	s__Sulfurimicrobium lacus	77.8879	209	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823025.1	s__Sulfuricella sp018823025	77.6196	157	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002424845.1	s__Thiobacillus denitrificans_F	77.4731	132	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549295.1	s__Azonexus sp900549295	77.1297	116	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.93	0.93	2	-
GCA_001899775.1	s__Thiobacillus sp001899775	77.0324	197	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864975.1	s__Sulfuriferula_A thiophila	76.9342	182	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835655.1	s__PFJX01 sp903835655	76.9317	137	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.87	99.69	0.96	0.90	25	-
GCA_016791205.1	s__Desulfobacillus sp016791205	76.7094	128	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112435.1	s__Novimethylophilus kurashikiensis	76.6103	100	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Novimethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	76.3209	119	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_016214175.1	s__JACRPB01 sp016214175	76.1211	101	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782025.1	s__Azonexus sp009782025	75.9986	93	1089	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:10,167] [INFO] GTDB search result was written to GCF_007992375.1_ASM799237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:10,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:10,173] [INFO] DFAST_QC result json was written to GCF_007992375.1_ASM799237v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:10,173] [INFO] DFAST_QC completed!
[2024-01-24 15:12:10,173] [INFO] Total running time: 0h1m16s