[2024-01-24 14:46:35,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,385] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference
[2024-01-24 14:46:36,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,671] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a785fcb-c8fb-44e4-914e-760b77e86ec4/GCF_009600605.1_ASM960060v1_genomic.fna.gz | prodigal -d GCF_009600605.1_ASM960060v1_genomic.fna/cds.fna -a GCF_009600605.1_ASM960060v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:51,594] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:51,594] [INFO] Task started: HMMsearch
[2024-01-24 14:46:51,594] [INFO] Running command: hmmsearch --tblout GCF_009600605.1_ASM960060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/reference_markers.hmm GCF_009600605.1_ASM960060v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:51,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:51,907] [INFO] Found 6/6 markers.
[2024-01-24 14:46:51,951] [INFO] Query marker FASTA was written to GCF_009600605.1_ASM960060v1_genomic.fna/markers.fasta
[2024-01-24 14:46:51,952] [INFO] Task started: Blastn
[2024-01-24 14:46:51,952] [INFO] Running command: blastn -query GCF_009600605.1_ASM960060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/reference_markers.fasta -out GCF_009600605.1_ASM960060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:53,360] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:53,364] [INFO] Selected 30 target genomes.
[2024-01-24 14:46:53,365] [INFO] Target genome list was writen to GCF_009600605.1_ASM960060v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:53,382] [INFO] Task started: fastANI
[2024-01-24 14:46:53,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a785fcb-c8fb-44e4-914e-760b77e86ec4/GCF_009600605.1_ASM960060v1_genomic.fna.gz --refList GCF_009600605.1_ASM960060v1_genomic.fna/target_genomes.txt --output GCF_009600605.1_ASM960060v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:21,777] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:21,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:21,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:21,800] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:21,800] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:21,800] [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
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.8484	576	1798	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.5958	580	1798	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.4624	700	1798	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.3036	498	1798	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	78.1297	421	1798	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	78.1033	521	1798	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.0805	508	1798	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	78.0183	511	1798	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.9854	374	1798	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.9633	548	1798	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.9398	360	1798	95	below_threshold
Amorphus coralli	strain=DSM 19760	GCA_000374525.1	340680	340680	type	True	77.9343	371	1798	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.8959	459	1798	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.8325	485	1798	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	77.7922	502	1798	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	77.705	520	1798	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.7015	367	1798	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.6836	450	1798	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6766	414	1798	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.6614	349	1798	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.6323	353	1798	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	77.5433	398	1798	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.4216	551	1798	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.3606	368	1798	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.3462	554	1798	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.2194	528	1798	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.1879	347	1798	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	77.0617	434	1798	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	77.0614	435	1798	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.9388	545	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:21,802] [INFO] DFAST Taxonomy check result was written to GCF_009600605.1_ASM960060v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:21,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:21,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:21,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/checkm_data
[2024-01-24 14:47:21,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:21,864] [INFO] Task started: CheckM
[2024-01-24 14:47:21,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009600605.1_ASM960060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009600605.1_ASM960060v1_genomic.fna/checkm_input GCF_009600605.1_ASM960060v1_genomic.fna/checkm_result
[2024-01-24 14:48:13,147] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:13,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:13,174] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:13,174] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:13,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009600605.1_ASM960060v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:13,175] [INFO] Task started: Blastn
[2024-01-24 14:48:13,175] [INFO] Running command: blastn -query GCF_009600605.1_ASM960060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf21aaf1-5210-4f33-bba7-4862e98741e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009600605.1_ASM960060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:15,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:15,348] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:15,348] [INFO] Target genome list was writen to GCF_009600605.1_ASM960060v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:15,365] [INFO] Task started: fastANI
[2024-01-24 14:48:15,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a785fcb-c8fb-44e4-914e-760b77e86ec4/GCF_009600605.1_ASM960060v1_genomic.fna.gz --refList GCF_009600605.1_ASM960060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009600605.1_ASM960060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:36,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:36,727] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:36,728] [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_009600605.1	s__Pseudoxanthobacter spirostomi	100.0	1797	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900148505.1	s__Pseudoxanthobacter soli	80.1263	766	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	78.442	700	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_016629525.1	s__Kaistia sp016629525	78.2355	510	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	78.1761	496	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013839445.1	s__Chthonobacter albigriseus	78.1555	418	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	78.1076	522	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	78.0959	505	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	77.9806	515	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_000374525.1	s__Amorphus coralli	77.9217	372	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.9088	362	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	77.8432	521	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390635.1	s__Ancylobacter_C lacus	77.8243	501	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	77.7822	398	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	77.7206	574	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCF_014201415.1	s__Chelatococcus_A composti	77.626	351	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_003173775.1	s__Methylobacterium sp003173775	77.5456	523	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_001043895.1	s__Methylobacterium indicum	77.4104	503	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_900185715.1	s__Bosea sp900185715	77.4097	500	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429505.1	s__Bosea sp001429505	77.327	449	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823325.1	s__Bosea sp013823325	77.0877	439	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.82	97.82	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:36,729] [INFO] GTDB search result was written to GCF_009600605.1_ASM960060v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:36,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:36,735] [INFO] DFAST_QC result json was written to GCF_009600605.1_ASM960060v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:36,736] [INFO] DFAST_QC completed!
[2024-01-24 14:48:36,736] [INFO] Total running time: 0h2m1s