[2024-01-24 10:47:40,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,786] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c4a9d9e-9f3e-4438-88db-30f273bd19ec/GCF_003730115.1_ASM373011v1_genomic.fna.gz | prodigal -d GCF_003730115.1_ASM373011v1_genomic.fna/cds.fna -a GCF_003730115.1_ASM373011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:53,271] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:53,271] [INFO] Task started: HMMsearch
[2024-01-24 10:47:53,271] [INFO] Running command: hmmsearch --tblout GCF_003730115.1_ASM373011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/reference_markers.hmm GCF_003730115.1_ASM373011v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:53,512] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:53,514] [INFO] Found 6/6 markers.
[2024-01-24 10:47:53,540] [INFO] Query marker FASTA was written to GCF_003730115.1_ASM373011v1_genomic.fna/markers.fasta
[2024-01-24 10:47:53,541] [INFO] Task started: Blastn
[2024-01-24 10:47:53,541] [INFO] Running command: blastn -query GCF_003730115.1_ASM373011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/reference_markers.fasta -out GCF_003730115.1_ASM373011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:54,408] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:54,412] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:54,412] [INFO] Target genome list was writen to GCF_003730115.1_ASM373011v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:54,423] [INFO] Task started: fastANI
[2024-01-24 10:47:54,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4a9d9e-9f3e-4438-88db-30f273bd19ec/GCF_003730115.1_ASM373011v1_genomic.fna.gz --refList GCF_003730115.1_ASM373011v1_genomic.fna/target_genomes.txt --output GCF_003730115.1_ASM373011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:04,569] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:04,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:04,582] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:04,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:04,583] [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
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	100.0	838	838	95	conclusive
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	78.2065	234	838	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	78.0653	230	838	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	77.971	228	838	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	77.5792	163	838	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	77.5368	201	838	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	77.5254	148	838	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	77.4727	186	838	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.2975	114	838	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.58	77	838	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	76.5746	85	838	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.4008	135	838	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.2037	98	838	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	76.0454	83	838	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	75.9874	74	838	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,586] [INFO] DFAST Taxonomy check result was written to GCF_003730115.1_ASM373011v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:04,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:04,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:04,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/checkm_data
[2024-01-24 10:48:04,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:04,621] [INFO] Task started: CheckM
[2024-01-24 10:48:04,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003730115.1_ASM373011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003730115.1_ASM373011v1_genomic.fna/checkm_input GCF_003730115.1_ASM373011v1_genomic.fna/checkm_result
[2024-01-24 10:48:34,562] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:34,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,586] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:34,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:34,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003730115.1_ASM373011v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:34,587] [INFO] Task started: Blastn
[2024-01-24 10:48:34,587] [INFO] Running command: blastn -query GCF_003730115.1_ASM373011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f79373-ba25-4c92-a4e4-fd62be943132/dqc_reference/reference_markers_gtdb.fasta -out GCF_003730115.1_ASM373011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:36,202] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:36,206] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:36,206] [INFO] Target genome list was writen to GCF_003730115.1_ASM373011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:36,220] [INFO] Task started: fastANI
[2024-01-24 10:48:36,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4a9d9e-9f3e-4438-88db-30f273bd19ec/GCF_003730115.1_ASM373011v1_genomic.fna.gz --refList GCF_003730115.1_ASM373011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003730115.1_ASM373011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:46,358] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,376] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:46,376] [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_003730115.1	s__Pseudomethylobacillus aquaticus	100.0	838	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	94.9799	712	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168195.1	s__CABHOJ01 sp902168195	79.3405	195	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CABHOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858335.1	s__Methylovorus glucosotrophus	78.2065	234	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylovorus	95.0	97.11	97.01	0.92	0.92	3	-
GCA_001704575.1	s__UBA6140 sp001704575	78.1153	229	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842435.1	s__UBA6140 sp002842435	78.0853	261	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842255.1	s__UBA6140 sp002842255	77.6813	147	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013705.1	s__Methylobacillus flagellatus	77.5871	164	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCF_000617925.1	s__Methylobacillus glycogenes	77.4586	186	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971475.1	s__Sulfuricella sp000971475	76.7584	91	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	76.5746	85	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141125.1	s__JABFRO01 sp013141125	76.5093	88	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JABFRO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663685.1	s__Cupriavidus necator_C	76.3212	116	838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,378] [INFO] GTDB search result was written to GCF_003730115.1_ASM373011v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:46,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:46,386] [INFO] DFAST_QC result json was written to GCF_003730115.1_ASM373011v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:46,386] [INFO] DFAST_QC completed!
[2024-01-24 10:48:46,386] [INFO] Total running time: 0h1m5s