[2024-01-24 13:13:11,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:11,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:11,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference
[2024-01-24 13:13:13,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,379] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c29e7e4-fa23-47be-986c-e3d3dee2ef6e/GCF_003148475.1_ASM314847v1_genomic.fna.gz | prodigal -d GCF_003148475.1_ASM314847v1_genomic.fna/cds.fna -a GCF_003148475.1_ASM314847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:28,519] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:28,520] [INFO] Task started: HMMsearch
[2024-01-24 13:13:28,520] [INFO] Running command: hmmsearch --tblout GCF_003148475.1_ASM314847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/reference_markers.hmm GCF_003148475.1_ASM314847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:28,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:28,892] [INFO] Found 6/6 markers.
[2024-01-24 13:13:28,953] [INFO] Query marker FASTA was written to GCF_003148475.1_ASM314847v1_genomic.fna/markers.fasta
[2024-01-24 13:13:28,954] [INFO] Task started: Blastn
[2024-01-24 13:13:28,954] [INFO] Running command: blastn -query GCF_003148475.1_ASM314847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/reference_markers.fasta -out GCF_003148475.1_ASM314847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:29,964] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:29,968] [INFO] Selected 29 target genomes.
[2024-01-24 13:13:29,969] [INFO] Target genome list was writen to GCF_003148475.1_ASM314847v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:30,737] [INFO] Task started: fastANI
[2024-01-24 13:13:30,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c29e7e4-fa23-47be-986c-e3d3dee2ef6e/GCF_003148475.1_ASM314847v1_genomic.fna.gz --refList GCF_003148475.1_ASM314847v1_genomic.fna/target_genomes.txt --output GCF_003148475.1_ASM314847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:06,605] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:06,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:06,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:06,639] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:06,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:06,639] [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 zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	81.6517	873	1591	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	80.9717	763	1591	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	80.7907	745	1591	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	80.4899	626	1591	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.4646	752	1591	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	80.4641	747	1591	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	80.4341	759	1591	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	80.3844	761	1591	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	80.3841	737	1591	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	80.2921	747	1591	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	80.2754	772	1591	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	80.263	705	1591	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	80.2548	776	1591	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	80.2525	731	1591	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.2217	731	1591	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	80.2054	744	1591	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	80.1725	763	1591	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.1233	777	1591	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	80.0789	615	1591	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.0085	711	1591	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.9908	719	1591	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.4463	615	1591	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2987	602	1591	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2678	606	1591	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.911	424	1591	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	77.7749	313	1591	95	below_threshold
Rhizobium gallicum	strain=R602	GCA_000816845.1	56730	56730	type	True	77.6291	300	1591	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	77.6024	312	1591	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	77.4282	317	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:06,641] [INFO] DFAST Taxonomy check result was written to GCF_003148475.1_ASM314847v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:06,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:06,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:06,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/checkm_data
[2024-01-24 13:14:06,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:06,687] [INFO] Task started: CheckM
[2024-01-24 13:14:06,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148475.1_ASM314847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148475.1_ASM314847v1_genomic.fna/checkm_input GCF_003148475.1_ASM314847v1_genomic.fna/checkm_result
[2024-01-24 13:14:52,980] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:52,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:53,002] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:53,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:53,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148475.1_ASM314847v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:53,003] [INFO] Task started: Blastn
[2024-01-24 13:14:53,003] [INFO] Running command: blastn -query GCF_003148475.1_ASM314847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8e7fb3-4198-4b50-b4bc-607051c4bf3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148475.1_ASM314847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:54,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:54,651] [INFO] Selected 20 target genomes.
[2024-01-24 13:14:54,651] [INFO] Target genome list was writen to GCF_003148475.1_ASM314847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:54,672] [INFO] Task started: fastANI
[2024-01-24 13:14:54,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c29e7e4-fa23-47be-986c-e3d3dee2ef6e/GCF_003148475.1_ASM314847v1_genomic.fna.gz --refList GCF_003148475.1_ASM314847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148475.1_ASM314847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:17,877] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:17,898] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:17,899] [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_003148475.1	s__Pseudaminobacter salicylatoxidans	100.0	1589	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	conclusive
GCF_003012705.1	s__Pseudaminobacter soli	84.4228	1012	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	83.3988	940	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	81.9256	841	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	81.6548	871	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	80.7907	745	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_004791025.1	s__Mesorhizobium sp004791025	80.7548	774	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	80.6921	763	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	80.5054	755	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCA_004791255.1	s__Mesorhizobium sp004791255	80.3853	732	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_003253745.1	s__Mesorhizobium kowhaii	80.36	768	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045125.1	s__Pseudaminobacter camelthorni	80.3438	743	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306585.1	s__Mesorhizobium sp017306585	80.2165	693	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170805.1	s__Mesorhizobium sp013170805	80.1725	773	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004017275.1	s__Mesorhizobium sp004017275	80.1692	736	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_014201615.1	s__Mesorhizobium lusatiense	80.0971	613	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305925.1	s__JAFKJW01 sp017305925	79.7761	595	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015500075.1	s__Mesorhizobium sp015500075	79.6866	723	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427285.1	s__Mesorhizobium sp001427285	79.6123	613	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176975.1	s__Aureimonas_A psammosilene	77.7634	315	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:17,900] [INFO] GTDB search result was written to GCF_003148475.1_ASM314847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:17,901] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:17,905] [INFO] DFAST_QC result json was written to GCF_003148475.1_ASM314847v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:17,905] [INFO] DFAST_QC completed!
[2024-01-24 13:15:17,906] [INFO] Total running time: 0h2m6s