[2024-01-24 13:01:39,568] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference
[2024-01-24 13:01:41,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,284] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dd14f0f-1fc0-4ddb-8774-cf2e66e893ad/GCF_003012745.1_ASM301274v1_genomic.fna.gz | prodigal -d GCF_003012745.1_ASM301274v1_genomic.fna/cds.fna -a GCF_003012745.1_ASM301274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:58,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:58,584] [INFO] Task started: HMMsearch
[2024-01-24 13:01:58,584] [INFO] Running command: hmmsearch --tblout GCF_003012745.1_ASM301274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/reference_markers.hmm GCF_003012745.1_ASM301274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:58,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:58,925] [INFO] Found 6/6 markers.
[2024-01-24 13:01:58,977] [INFO] Query marker FASTA was written to GCF_003012745.1_ASM301274v1_genomic.fna/markers.fasta
[2024-01-24 13:01:58,978] [INFO] Task started: Blastn
[2024-01-24 13:01:58,978] [INFO] Running command: blastn -query GCF_003012745.1_ASM301274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/reference_markers.fasta -out GCF_003012745.1_ASM301274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:00,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:00,089] [INFO] Selected 23 target genomes.
[2024-01-24 13:02:00,089] [INFO] Target genome list was writen to GCF_003012745.1_ASM301274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:00,096] [INFO] Task started: fastANI
[2024-01-24 13:02:00,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd14f0f-1fc0-4ddb-8774-cf2e66e893ad/GCF_003012745.1_ASM301274v1_genomic.fna.gz --refList GCF_003012745.1_ASM301274v1_genomic.fna/target_genomes.txt --output GCF_003012745.1_ASM301274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:32,100] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:32,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:32,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:32,128] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:32,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:32,129] [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 silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	81.3774	889	1995	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	81.35	890	1995	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	81.2114	976	1995	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	81.0997	929	1995	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	81.0973	931	1995	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	80.9876	901	1995	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	80.9657	999	1995	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.952	1003	1995	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	80.8725	996	1995	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.8671	973	1995	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	80.8415	936	1995	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.8099	886	1995	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	80.7422	939	1995	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.7358	960	1995	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.5692	1037	1995	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	80.5469	968	1995	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.5141	901	1995	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.4962	894	1995	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	80.4629	853	1995	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	80.4197	909	1995	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.8323	732	1995	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	79.7543	631	1995	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.4899	686	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:32,131] [INFO] DFAST Taxonomy check result was written to GCF_003012745.1_ASM301274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:32,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:32,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:32,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/checkm_data
[2024-01-24 13:02:32,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:32,199] [INFO] Task started: CheckM
[2024-01-24 13:02:32,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012745.1_ASM301274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012745.1_ASM301274v1_genomic.fna/checkm_input GCF_003012745.1_ASM301274v1_genomic.fna/checkm_result
[2024-01-24 13:03:22,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:22,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:22,101] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:22,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:22,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012745.1_ASM301274v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:22,102] [INFO] Task started: Blastn
[2024-01-24 13:03:22,103] [INFO] Running command: blastn -query GCF_003012745.1_ASM301274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814eba86-591f-45f9-b2c1-eeac3d4d6e0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012745.1_ASM301274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:24,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:24,295] [INFO] Selected 22 target genomes.
[2024-01-24 13:03:24,296] [INFO] Target genome list was writen to GCF_003012745.1_ASM301274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:24,313] [INFO] Task started: fastANI
[2024-01-24 13:03:24,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd14f0f-1fc0-4ddb-8774-cf2e66e893ad/GCF_003012745.1_ASM301274v1_genomic.fna.gz --refList GCF_003012745.1_ASM301274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012745.1_ASM301274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:52,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:52,995] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:52,995] [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_003012745.1	s__Mesorhizobium_D ephedrae	100.0	1988	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016756535.1	s__Mesorhizobium sp016756535	81.3624	1023	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	81.2075	951	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863365.1	s__Mesorhizobium tamadayense	81.1938	981	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	81.1653	790	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306545.1	s__Mesorhizobium sp017306545	81.1249	867	1995	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	81.1062	999	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_014595955.1	s__Mesorhizobium_D sp014595955	81.0869	932	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	81.0201	649	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206975.1	s__Aminobacter aganoensis	80.9626	905	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_004016445.2	s__Mesorhizobium sp004016445	80.8961	993	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_000350085.1	s__Mesorhizobium metallidurans	80.8716	972	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034915.1	s__Mesorhizobium helmanticense	80.854	999	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.01	95.01	0.86	0.86	2	-
GCF_014200015.1	s__Aminobacter niigataensis	80.7788	889	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCA_905339215.1	s__DUSC01 sp008933895	80.7041	807	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	80.6774	872	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	80.5928	422	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	80.5785	846	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727715.1	s__Mesorhizobium terrae	80.5457	893	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCA_012842935.1	s__DUSC01 sp012842935	80.3211	688	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	80.2414	794	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336975.1	s__Mesorhizobium_A sp002336975	79.6543	550	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:52,997] [INFO] GTDB search result was written to GCF_003012745.1_ASM301274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:52,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:53,002] [INFO] DFAST_QC result json was written to GCF_003012745.1_ASM301274v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:53,002] [INFO] DFAST_QC completed!
[2024-01-24 13:03:53,002] [INFO] Total running time: 0h2m13s