[2024-01-24 12:22:14,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference
[2024-01-24 12:22:15,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,714] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ab6b378-f801-49b7-8792-4d1bbcaf814a/GCF_009858335.1_ASM985833v1_genomic.fna.gz | prodigal -d GCF_009858335.1_ASM985833v1_genomic.fna/cds.fna -a GCF_009858335.1_ASM985833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:25,720] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:25,721] [INFO] Task started: HMMsearch
[2024-01-24 12:22:25,721] [INFO] Running command: hmmsearch --tblout GCF_009858335.1_ASM985833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/reference_markers.hmm GCF_009858335.1_ASM985833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:26,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:26,080] [INFO] Found 6/6 markers.
[2024-01-24 12:22:26,117] [INFO] Query marker FASTA was written to GCF_009858335.1_ASM985833v1_genomic.fna/markers.fasta
[2024-01-24 12:22:26,117] [INFO] Task started: Blastn
[2024-01-24 12:22:26,117] [INFO] Running command: blastn -query GCF_009858335.1_ASM985833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/reference_markers.fasta -out GCF_009858335.1_ASM985833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:27,007] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:27,010] [INFO] Selected 8 target genomes.
[2024-01-24 12:22:27,010] [INFO] Target genome list was writen to GCF_009858335.1_ASM985833v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:27,018] [INFO] Task started: fastANI
[2024-01-24 12:22:27,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab6b378-f801-49b7-8792-4d1bbcaf814a/GCF_009858335.1_ASM985833v1_genomic.fna.gz --refList GCF_009858335.1_ASM985833v1_genomic.fna/target_genomes.txt --output GCF_009858335.1_ASM985833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:32,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:32,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:32,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:32,013] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:32,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:32,014] [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
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	100.0	968	968	95	conclusive
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	91.4553	845	968	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	89.9147	867	968	95	below_threshold
Methylobacillus methanolivorans	strain=VKM B-3037	GCA_020531845.1	1848927	1848927	type	True	78.1804	214	968	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	78.1646	209	968	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	78.0197	241	968	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	77.9379	283	968	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	77.5196	202	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,017] [INFO] DFAST Taxonomy check result was written to GCF_009858335.1_ASM985833v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:32,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:32,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:32,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/checkm_data
[2024-01-24 12:22:32,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:32,050] [INFO] Task started: CheckM
[2024-01-24 12:22:32,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009858335.1_ASM985833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009858335.1_ASM985833v1_genomic.fna/checkm_input GCF_009858335.1_ASM985833v1_genomic.fna/checkm_result
[2024-01-24 12:23:06,228] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:06,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,261] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:06,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:06,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009858335.1_ASM985833v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:06,262] [INFO] Task started: Blastn
[2024-01-24 12:23:06,262] [INFO] Running command: blastn -query GCF_009858335.1_ASM985833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27ac6408-7762-4a3a-8436-433047169d12/dqc_reference/reference_markers_gtdb.fasta -out GCF_009858335.1_ASM985833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:07,562] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:07,565] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:07,566] [INFO] Target genome list was writen to GCF_009858335.1_ASM985833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:07,577] [INFO] Task started: fastANI
[2024-01-24 12:23:07,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab6b378-f801-49b7-8792-4d1bbcaf814a/GCF_009858335.1_ASM985833v1_genomic.fna.gz --refList GCF_009858335.1_ASM985833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009858335.1_ASM985833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:14,867] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:14,884] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:14,884] [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_009858335.1	s__Methylovorus glucosotrophus	100.0	968	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylovorus	95.0	97.11	97.01	0.92	0.92	3	conclusive
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	78.2717	239	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187985.1	s__Methylobacillus rhizosphaerae	77.9571	190	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617925.1	s__Methylobacillus glycogenes	77.9379	283	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648895.1	s__MM1 sp001648895	77.8906	113	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__MM1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168195.1	s__CABHOJ01 sp902168195	77.757	176	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CABHOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339275.1	s__UBA6140 sp905339275	77.722	225	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645185.1	s__MM2 sp001645185	77.6658	203	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__MM2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842435.1	s__UBA6140 sp002842435	77.6121	214	968	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	77.5052	203	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCA_002479405.1	s__UBA6140 sp002479405	77.4474	183	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704575.1	s__UBA6140 sp001704575	77.4239	191	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880825.1	s__JADGRN01 sp017880825	77.2397	123	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JADGRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842135.1	s__UBA6140 sp002842135	77.113	155	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824575.1	s__CAIJXJ01 sp903824575	76.5042	104	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CAIJXJ01	95.0	99.81	99.81	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:14,887] [INFO] GTDB search result was written to GCF_009858335.1_ASM985833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:14,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:14,890] [INFO] DFAST_QC result json was written to GCF_009858335.1_ASM985833v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:14,891] [INFO] DFAST_QC completed!
[2024-01-24 12:23:14,891] [INFO] Total running time: 0h1m1s