[2024-01-24 12:47:14,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:14,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:14,107] [INFO] DQC Reference Directory: /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference
[2024-01-24 12:47:15,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,512] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,512] [INFO] Running command: gunzip -c /var/lib/cwl/stgcefb80dc-7185-4d55-baaf-49fa452fe81f/GCF_000218565.1_ASM21856v1_genomic.fna.gz | prodigal -d GCF_000218565.1_ASM21856v1_genomic.fna/cds.fna -a GCF_000218565.1_ASM21856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:28,063] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:28,063] [INFO] Task started: HMMsearch
[2024-01-24 12:47:28,063] [INFO] Running command: hmmsearch --tblout GCF_000218565.1_ASM21856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/reference_markers.hmm GCF_000218565.1_ASM21856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:28,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:28,401] [INFO] Found 6/6 markers.
[2024-01-24 12:47:28,457] [INFO] Query marker FASTA was written to GCF_000218565.1_ASM21856v1_genomic.fna/markers.fasta
[2024-01-24 12:47:28,458] [INFO] Task started: Blastn
[2024-01-24 12:47:28,458] [INFO] Running command: blastn -query GCF_000218565.1_ASM21856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/reference_markers.fasta -out GCF_000218565.1_ASM21856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:29,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:29,404] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:29,404] [INFO] Target genome list was writen to GCF_000218565.1_ASM21856v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:29,428] [INFO] Task started: fastANI
[2024-01-24 12:47:29,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgcefb80dc-7185-4d55-baaf-49fa452fe81f/GCF_000218565.1_ASM21856v1_genomic.fna.gz --refList GCF_000218565.1_ASM21856v1_genomic.fna/target_genomes.txt --output GCF_000218565.1_ASM21856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:53,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:53,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:53,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:53,592] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:53,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:53,592] [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
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	100.0	1297	1297	95	conclusive
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	99.9918	1247	1297	95	conclusive
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	83.6887	874	1297	95	below_threshold
Afipia felis	strain=NCTC12499	GCA_900445155.1	1035	1035	type	True	83.6841	870	1297	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	79.9941	564	1297	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	79.7648	604	1297	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.7022	562	1297	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.6211	552	1297	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	79.6037	547	1297	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	79.5946	541	1297	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.5671	535	1297	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	79.5458	520	1297	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	79.5385	579	1297	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	79.4405	544	1297	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	79.3581	560	1297	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	79.3537	535	1297	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.3335	541	1297	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	79.2483	537	1297	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	77.2657	187	1297	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	76.8407	178	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:53,594] [INFO] DFAST Taxonomy check result was written to GCF_000218565.1_ASM21856v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:53,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:53,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:53,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/checkm_data
[2024-01-24 12:47:53,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:53,639] [INFO] Task started: CheckM
[2024-01-24 12:47:53,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000218565.1_ASM21856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000218565.1_ASM21856v1_genomic.fna/checkm_input GCF_000218565.1_ASM21856v1_genomic.fna/checkm_result
[2024-01-24 12:48:32,148] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:32,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:32,175] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:32,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:32,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000218565.1_ASM21856v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:32,176] [INFO] Task started: Blastn
[2024-01-24 12:48:32,176] [INFO] Running command: blastn -query GCF_000218565.1_ASM21856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d5e8f4-81ce-49d8-b7e3-a1948c430d9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000218565.1_ASM21856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:33,883] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:33,887] [INFO] Selected 18 target genomes.
[2024-01-24 12:48:33,887] [INFO] Target genome list was writen to GCF_000218565.1_ASM21856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:33,905] [INFO] Task started: fastANI
[2024-01-24 12:48:33,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgcefb80dc-7185-4d55-baaf-49fa452fe81f/GCF_000218565.1_ASM21856v1_genomic.fna.gz --refList GCF_000218565.1_ASM21856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000218565.1_ASM21856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:50,898] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:50,918] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:50,918] [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_000218565.1	s__Afipia carboxidovorans	100.0	1297	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_000178995.1	s__Afipia sp000178995	84.0126	858	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.46	98.22	0.89	0.84	3	-
GCF_000314735.2	s__Afipia felis	83.6991	873	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.60	95.79	0.96	0.87	4	-
GCA_001897755.1	s__Afipia sp001897755	82.1734	705	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017305455.1	s__Afipia sp017305455	81.7598	683	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425835.1	s__Afipia sp001425835	80.6684	622	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308575.1	s__Afipia sp001897905	80.184	604	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
GCF_018131225.1	s__U87765 sp018131225	79.6161	583	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__U87765	95.0	100.00	100.00	1.00	1.00	5	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	79.5916	541	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCA_017474385.1	s__Afipia sp017474385	79.5914	435	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900218015.1	s__Rhodopseudomonas pentothenatexigens	79.556	518	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_018130945.1	s__Bradyrhizobium manausense_C	79.4623	553	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177255.2	s__Rhodopseudomonas palustris_G	79.3972	533	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.28	98.19	0.96	0.95	4	-
GCF_000516555.1	s__P52-10 sp000516555	79.1286	477	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__P52-10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980495.1	s__Paramesorhizobium phragmitis	77.2812	186	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200175.1	s__Rhizobium lentis_A	76.9624	179	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCA_019244955.1	s__JAFASC01 sp019244955	76.8216	131	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__JAFASC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829155.1	s__Rhizobium sp900467885	76.7375	143	1297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.99	98.86	0.92	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:50,919] [INFO] GTDB search result was written to GCF_000218565.1_ASM21856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:50,920] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:50,925] [INFO] DFAST_QC result json was written to GCF_000218565.1_ASM21856v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:50,925] [INFO] DFAST_QC completed!
[2024-01-24 12:48:50,926] [INFO] Total running time: 0h1m37s