[2024-01-24 13:09:29,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference
[2024-01-24 13:09:30,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,400] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d704921-0f28-49de-9012-c387b25f74bb/GCF_000013705.1_ASM1370v1_genomic.fna.gz | prodigal -d GCF_000013705.1_ASM1370v1_genomic.fna/cds.fna -a GCF_000013705.1_ASM1370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:40,684] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:40,684] [INFO] Task started: HMMsearch
[2024-01-24 13:09:40,685] [INFO] Running command: hmmsearch --tblout GCF_000013705.1_ASM1370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/reference_markers.hmm GCF_000013705.1_ASM1370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:40,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:40,975] [INFO] Found 6/6 markers.
[2024-01-24 13:09:41,007] [INFO] Query marker FASTA was written to GCF_000013705.1_ASM1370v1_genomic.fna/markers.fasta
[2024-01-24 13:09:41,008] [INFO] Task started: Blastn
[2024-01-24 13:09:41,008] [INFO] Running command: blastn -query GCF_000013705.1_ASM1370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/reference_markers.fasta -out GCF_000013705.1_ASM1370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:41,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:41,816] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:41,816] [INFO] Target genome list was writen to GCF_000013705.1_ASM1370v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:41,824] [INFO] Task started: fastANI
[2024-01-24 13:09:41,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d704921-0f28-49de-9012-c387b25f74bb/GCF_000013705.1_ASM1370v1_genomic.fna.gz --refList GCF_000013705.1_ASM1370v1_genomic.fna/target_genomes.txt --output GCF_000013705.1_ASM1370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:51,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:51,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:51,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:51,280] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:51,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:51,281] [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
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	100.0	971	990	95	conclusive
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	80.748	588	990	95	below_threshold
Methylobacillus methanolivorans	strain=VKM B-3037	GCA_020531845.1	1848927	1848927	type	True	80.4585	573	990	95	below_threshold
Methylobacillus rhizosphaerae	strain=Ca-68	GCA_900187985.1	551994	551994	type	True	79.2687	374	990	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	78.678	391	990	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	78.5709	363	990	95	below_threshold
Methylobacillus gramineus	strain=VKM B-2591	GCA_020532675.1	755169	755169	type	True	78.2707	325	990	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	77.7056	203	990	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.6658	169	990	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	77.5651	198	990	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	77.3934	183	990	95	below_threshold
Novimethylophilus kurashikiensis	strain=La2-4	GCA_003112435.1	1825523	1825523	type	True	77.1281	119	990	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	76.8673	59	990	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	76.5702	54	990	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.4351	57	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:51,282] [INFO] DFAST Taxonomy check result was written to GCF_000013705.1_ASM1370v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:51,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:51,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:51,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/checkm_data
[2024-01-24 13:09:51,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:51,320] [INFO] Task started: CheckM
[2024-01-24 13:09:51,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013705.1_ASM1370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013705.1_ASM1370v1_genomic.fna/checkm_input GCF_000013705.1_ASM1370v1_genomic.fna/checkm_result
[2024-01-24 13:10:26,605] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:26,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:26,627] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:26,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:26,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013705.1_ASM1370v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:26,628] [INFO] Task started: Blastn
[2024-01-24 13:10:26,628] [INFO] Running command: blastn -query GCF_000013705.1_ASM1370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05752d0d-413b-4c1a-8727-9a6d01234708/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013705.1_ASM1370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:27,895] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:27,898] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:27,898] [INFO] Target genome list was writen to GCF_000013705.1_ASM1370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:27,942] [INFO] Task started: fastANI
[2024-01-24 13:10:27,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d704921-0f28-49de-9012-c387b25f74bb/GCF_000013705.1_ASM1370v1_genomic.fna.gz --refList GCF_000013705.1_ASM1370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013705.1_ASM1370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,589] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,590] [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_000013705.1	s__Methylobacillus flagellatus	100.0	972	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	conclusive
GCF_900187985.1	s__Methylobacillus rhizosphaerae	79.2634	373	990	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	78.5709	363	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	77.7374	178	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730115.1	s__Pseudomethylobacillus aquaticus	77.6707	168	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858335.1	s__Methylovorus glucosotrophus	77.5687	197	990	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	77.5268	154	990	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	77.374	164	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339275.1	s__UBA6140 sp905339275	77.3614	186	990	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	77.254	81	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JADGRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112435.1	s__Novimethylophilus kurashikiensis	77.1516	118	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Novimethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842255.1	s__UBA6140 sp002842255	76.9025	97	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297055.2	s__Sulfuricella denitrificans	76.8617	62	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479405.1	s__UBA6140 sp002479405	76.8599	154	990	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,596] [INFO] GTDB search result was written to GCF_000013705.1_ASM1370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,600] [INFO] DFAST_QC result json was written to GCF_000013705.1_ASM1370v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,601] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,601] [INFO] Total running time: 0h1m5s