[2024-01-24 15:27:41,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c3141e3-5e22-486c-9aeb-80b60f2420bd/GCF_027922265.1_ASM2792226v1_genomic.fna.gz | prodigal -d GCF_027922265.1_ASM2792226v1_genomic.fna/cds.fna -a GCF_027922265.1_ASM2792226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:53,384] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:53,385] [INFO] Task started: HMMsearch
[2024-01-24 15:27:53,385] [INFO] Running command: hmmsearch --tblout GCF_027922265.1_ASM2792226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/reference_markers.hmm GCF_027922265.1_ASM2792226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:53,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:53,668] [INFO] Found 6/6 markers.
[2024-01-24 15:27:53,711] [INFO] Query marker FASTA was written to GCF_027922265.1_ASM2792226v1_genomic.fna/markers.fasta
[2024-01-24 15:27:53,711] [INFO] Task started: Blastn
[2024-01-24 15:27:53,712] [INFO] Running command: blastn -query GCF_027922265.1_ASM2792226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/reference_markers.fasta -out GCF_027922265.1_ASM2792226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,677] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,684] [INFO] Selected 31 target genomes.
[2024-01-24 15:27:54,684] [INFO] Target genome list was writen to GCF_027922265.1_ASM2792226v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:54,721] [INFO] Task started: fastANI
[2024-01-24 15:27:54,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3141e3-5e22-486c-9aeb-80b60f2420bd/GCF_027922265.1_ASM2792226v1_genomic.fna.gz --refList GCF_027922265.1_ASM2792226v1_genomic.fna/target_genomes.txt --output GCF_027922265.1_ASM2792226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:22,284] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:22,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:22,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:22,311] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:28:22,311] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:28:22,311] [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
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	82.0095	739	1262	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	78.2334	363	1262	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1358	306	1262	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	78.13	430	1262	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.1236	394	1262	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	78.0382	398	1262	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	78.0212	427	1262	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	78.0168	334	1262	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	77.958	403	1262	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.9576	396	1262	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	77.8983	373	1262	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	77.8416	381	1262	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.823	436	1262	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.8207	470	1262	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.8092	355	1262	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.7928	444	1262	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.6943	444	1262	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6631	318	1262	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.6245	339	1262	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	77.6093	408	1262	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.5749	418	1262	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.5079	363	1262	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.4859	405	1262	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.4751	308	1262	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.4272	413	1262	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.3496	361	1262	95	below_threshold
Tepidamorphus gemmatus	strain=DSM 19345	GCA_004346195.1	747076	747076	type	True	77.3378	252	1262	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.988	142	1262	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	75.4552	51	1262	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	74.8721	138	1262	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	74.8053	145	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:22,313] [INFO] DFAST Taxonomy check result was written to GCF_027922265.1_ASM2792226v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:22,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:22,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:22,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/checkm_data
[2024-01-24 15:28:22,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:22,368] [INFO] Task started: CheckM
[2024-01-24 15:28:22,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922265.1_ASM2792226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922265.1_ASM2792226v1_genomic.fna/checkm_input GCF_027922265.1_ASM2792226v1_genomic.fna/checkm_result
[2024-01-24 15:28:52,823] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:52,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:52,850] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:52,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:52,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922265.1_ASM2792226v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:52,853] [INFO] Task started: Blastn
[2024-01-24 15:28:52,853] [INFO] Running command: blastn -query GCF_027922265.1_ASM2792226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg105f4df2-6c32-47a2-9d5c-b4c7e8132b4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922265.1_ASM2792226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:54,605] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:54,608] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:54,609] [INFO] Target genome list was writen to GCF_027922265.1_ASM2792226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:54,622] [INFO] Task started: fastANI
[2024-01-24 15:28:54,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3141e3-5e22-486c-9aeb-80b60f2420bd/GCF_027922265.1_ASM2792226v1_genomic.fna.gz --refList GCF_027922265.1_ASM2792226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922265.1_ASM2792226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:06,031] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:06,044] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:29:06,045] [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_004310425.1	s__Hansschlegelia quercus	82.4037	795	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	81.9817	742	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	81.5939	751	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907975.1	s__Methylopila capsulata	81.5639	741	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	81.5283	771	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	81.5144	693	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	81.4277	751	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384475.1	s__Hansschlegelia sp000384475	81.3753	747	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	81.1586	718	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197755.1	s__Ferrovibrio terrae	77.0045	141	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851655.1	s__CAIMFV01 sp903851655	76.5856	110	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
GCA_017991315.1	s__Ferrovibrio sp017991315	76.3965	91	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694165.1	s__SHVP01 sp009694165	75.8355	57	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVP01;f__SHVP01;g__SHVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	75.0802	86	1262	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:06,047] [INFO] GTDB search result was written to GCF_027922265.1_ASM2792226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:06,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:06,052] [INFO] DFAST_QC result json was written to GCF_027922265.1_ASM2792226v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:06,052] [INFO] DFAST_QC completed!
[2024-01-24 15:29:06,052] [INFO] Total running time: 0h1m25s