[2024-01-25 17:53:50,412] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference
[2024-01-25 17:53:51,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,610] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,611] [INFO] Running command: gunzip -c /var/lib/cwl/stga6453959-73a5-4cfd-8bc3-81a386b19cfe/GCF_014645695.1_ASM1464569v1_genomic.fna.gz | prodigal -d GCF_014645695.1_ASM1464569v1_genomic.fna/cds.fna -a GCF_014645695.1_ASM1464569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:03,629] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:03,629] [INFO] Task started: HMMsearch
[2024-01-25 17:54:03,629] [INFO] Running command: hmmsearch --tblout GCF_014645695.1_ASM1464569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/reference_markers.hmm GCF_014645695.1_ASM1464569v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:03,873] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:03,875] [INFO] Found 6/6 markers.
[2024-01-25 17:54:03,917] [INFO] Query marker FASTA was written to GCF_014645695.1_ASM1464569v1_genomic.fna/markers.fasta
[2024-01-25 17:54:03,918] [INFO] Task started: Blastn
[2024-01-25 17:54:03,918] [INFO] Running command: blastn -query GCF_014645695.1_ASM1464569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/reference_markers.fasta -out GCF_014645695.1_ASM1464569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:04,989] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:04,991] [INFO] Selected 23 target genomes.
[2024-01-25 17:54:04,991] [INFO] Target genome list was writen to GCF_014645695.1_ASM1464569v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:05,004] [INFO] Task started: fastANI
[2024-01-25 17:54:05,005] [INFO] Running command: fastANI --query /var/lib/cwl/stga6453959-73a5-4cfd-8bc3-81a386b19cfe/GCF_014645695.1_ASM1464569v1_genomic.fna.gz --refList GCF_014645695.1_ASM1464569v1_genomic.fna/target_genomes.txt --output GCF_014645695.1_ASM1464569v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:30,584] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:30,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:30,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:30,598] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:30,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:30,598] [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
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	100.0	1681	1684	95	conclusive
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	86.4594	1210	1684	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.2645	695	1684	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	78.7179	489	1684	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.7012	629	1684	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	78.6231	502	1684	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	78.3393	532	1684	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	78.3294	534	1684	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	78.3105	503	1684	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	78.3066	633	1684	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	78.2755	696	1684	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	78.2401	584	1684	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	78.2187	592	1684	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.1938	667	1684	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	78.1878	543	1684	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	78.1868	610	1684	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	78.0919	593	1684	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	78.0459	560	1684	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	78.0115	544	1684	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	77.9855	435	1684	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.8562	432	1684	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	77.813	542	1684	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	77.7889	487	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:30,600] [INFO] DFAST Taxonomy check result was written to GCF_014645695.1_ASM1464569v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:30,601] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:30,601] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:30,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/checkm_data
[2024-01-25 17:54:30,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:30,647] [INFO] Task started: CheckM
[2024-01-25 17:54:30,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645695.1_ASM1464569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645695.1_ASM1464569v1_genomic.fna/checkm_input GCF_014645695.1_ASM1464569v1_genomic.fna/checkm_result
[2024-01-25 17:55:30,150] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:30,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:30,175] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:30,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:30,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645695.1_ASM1464569v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:30,176] [INFO] Task started: Blastn
[2024-01-25 17:55:30,177] [INFO] Running command: blastn -query GCF_014645695.1_ASM1464569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb73dee-a0f7-4665-ab80-159c105f765d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645695.1_ASM1464569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:32,411] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:32,414] [INFO] Selected 19 target genomes.
[2024-01-25 17:55:32,414] [INFO] Target genome list was writen to GCF_014645695.1_ASM1464569v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:32,433] [INFO] Task started: fastANI
[2024-01-25 17:55:32,433] [INFO] Running command: fastANI --query /var/lib/cwl/stga6453959-73a5-4cfd-8bc3-81a386b19cfe/GCF_014645695.1_ASM1464569v1_genomic.fna.gz --refList GCF_014645695.1_ASM1464569v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645695.1_ASM1464569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:54,349] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:54,361] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:54,361] [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_014645695.1	s__Salinarimonas ramus	100.0	1681	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000429045.1	s__Salinarimonas rosea	86.4504	1211	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693435.1	s__Salinarimonas sp007693435	79.1593	527	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	78.8025	522	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.7104	631	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_009363855.1	s__Microvirga thermotolerans	78.6805	493	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567055.1	s__Salinarimonas sp003567055	78.5272	350	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	78.337	533	1684	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_001653715.1	s__Methylobacterium platani	78.3092	690	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCA_900466745.1	s__Bosea sp900466745	78.2119	559	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_003173775.1	s__Methylobacterium sp003173775	78.1951	680	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_000022085.1	s__Methylobacterium nodulans	78.1652	615	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	78.163	549	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_001713455.1	s__Bosea sp001713455	78.1441	556	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCA_002279705.1	s__Bosea sp002279705	78.0922	493	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.41	99.41	0.89	0.89	2	-
GCF_000019365.1	s__Methylobacterium sp000019365	78.0175	699	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_003173715.1	s__Methylobacterium durans	78.0116	565	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	77.8016	545	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	77.7313	570	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:54,362] [INFO] GTDB search result was written to GCF_014645695.1_ASM1464569v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:54,363] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:54,366] [INFO] DFAST_QC result json was written to GCF_014645695.1_ASM1464569v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:54,366] [INFO] DFAST_QC completed!
[2024-01-25 17:55:54,366] [INFO] Total running time: 0h2m4s