[2024-01-24 12:42:09,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference
[2024-01-24 12:42:10,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,482] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdfc03b7-f56a-4a81-a7ce-2bc4f687bf12/GCF_002075885.1_ASM207588v1_genomic.fna.gz | prodigal -d GCF_002075885.1_ASM207588v1_genomic.fna/cds.fna -a GCF_002075885.1_ASM207588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:25,237] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:25,238] [INFO] Task started: HMMsearch
[2024-01-24 12:42:25,238] [INFO] Running command: hmmsearch --tblout GCF_002075885.1_ASM207588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/reference_markers.hmm GCF_002075885.1_ASM207588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:25,538] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:25,539] [INFO] Found 6/6 markers.
[2024-01-24 12:42:25,585] [INFO] Query marker FASTA was written to GCF_002075885.1_ASM207588v1_genomic.fna/markers.fasta
[2024-01-24 12:42:25,585] [INFO] Task started: Blastn
[2024-01-24 12:42:25,585] [INFO] Running command: blastn -query GCF_002075885.1_ASM207588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/reference_markers.fasta -out GCF_002075885.1_ASM207588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:26,522] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:26,525] [INFO] Selected 27 target genomes.
[2024-01-24 12:42:26,526] [INFO] Target genome list was writen to GCF_002075885.1_ASM207588v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:26,551] [INFO] Task started: fastANI
[2024-01-24 12:42:26,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdfc03b7-f56a-4a81-a7ce-2bc4f687bf12/GCF_002075885.1_ASM207588v1_genomic.fna.gz --refList GCF_002075885.1_ASM207588v1_genomic.fna/target_genomes.txt --output GCF_002075885.1_ASM207588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:57,109] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:57,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:57,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:57,129] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:42:57,130] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:42:57,130] [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
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	80.7395	751	1586	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.1042	730	1586	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.9869	717	1586	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	79.9731	732	1586	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	79.9158	764	1586	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.9157	768	1586	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	79.8734	760	1586	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	79.85	788	1586	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.8244	736	1586	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	79.8128	732	1586	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.7909	703	1586	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.7884	768	1586	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	79.7805	737	1586	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	79.78	737	1586	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	79.7481	751	1586	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	79.7281	744	1586	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.7066	707	1586	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	79.6883	721	1586	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	79.5925	590	1586	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.4418	634	1586	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	79.0463	645	1586	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	79.0394	642	1586	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	79.0291	594	1586	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.9077	589	1586	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.3072	464	1586	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.282	466	1586	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.0196	442	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:57,131] [INFO] DFAST Taxonomy check result was written to GCF_002075885.1_ASM207588v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:57,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:57,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:57,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/checkm_data
[2024-01-24 12:42:57,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:57,182] [INFO] Task started: CheckM
[2024-01-24 12:42:57,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002075885.1_ASM207588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002075885.1_ASM207588v1_genomic.fna/checkm_input GCF_002075885.1_ASM207588v1_genomic.fna/checkm_result
[2024-01-24 12:43:41,474] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:41,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:41,501] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:41,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:41,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002075885.1_ASM207588v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:41,503] [INFO] Task started: Blastn
[2024-01-24 12:43:41,503] [INFO] Running command: blastn -query GCF_002075885.1_ASM207588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d071393-19e0-4cd2-a572-9b7d2003d1e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002075885.1_ASM207588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:43,302] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:43,307] [INFO] Selected 26 target genomes.
[2024-01-24 12:43:43,307] [INFO] Target genome list was writen to GCF_002075885.1_ASM207588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:43,373] [INFO] Task started: fastANI
[2024-01-24 12:43:43,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdfc03b7-f56a-4a81-a7ce-2bc4f687bf12/GCF_002075885.1_ASM207588v1_genomic.fna.gz --refList GCF_002075885.1_ASM207588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002075885.1_ASM207588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:14,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:14,495] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:14,495] [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_002075885.1	s__Mesorhizobium manganicum	100.0	1576	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004801285.1	s__Mesorhizobium composti	80.7484	750	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_016756535.1	s__Mesorhizobium sp016756535	80.1765	764	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	80.1338	762	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003952505.1	s__Mesorhizobium sp003952505	80.1026	732	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_000350085.1	s__Mesorhizobium metallidurans	80.0917	730	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843845.1	s__Mesorhizobium amorphae_A	80.0746	746	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	97.39	97.39	0.88	0.88	2	-
GCF_003952465.1	s__Mesorhizobium sp003952465	80.0626	756	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_008727715.1	s__Mesorhizobium terrae	79.9609	735	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCF_000359125.1	s__Mesorhizobium sp000359125	79.9516	701	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	79.949	760	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_000824845.1	s__Mesorhizobium sp000824845	79.9337	703	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601975.1	s__Mesorhizobium waimense	79.9301	766	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	79.8977	724	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919685.1	s__Mesorhizobium norvegicum	79.8931	758	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_013170705.1	s__Mesorhizobium loti_D	79.8164	743	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
GCF_003148495.1	s__Mesorhizobium loti	79.7985	736	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.10	97.93	0.88	0.86	3	-
GCF_000427725.1	s__Mesorhizobium sp000427725	79.7978	757	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427385.1	s__Mesorhizobium sp001427385	79.7533	641	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791255.1	s__Mesorhizobium sp004791255	79.7259	740	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.6096	636	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_004363725.1	s__Mesorhizobium defluvii	79.6068	592	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	79.4512	632	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	79.0887	651	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045125.1	s__Pseudaminobacter camelthorni	78.8761	624	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	78.841	564	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:14,497] [INFO] GTDB search result was written to GCF_002075885.1_ASM207588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:14,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:14,508] [INFO] DFAST_QC result json was written to GCF_002075885.1_ASM207588v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:14,509] [INFO] DFAST_QC completed!
[2024-01-24 12:44:14,509] [INFO] Total running time: 0h2m5s