[2024-01-24 13:17:27,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference
[2024-01-24 13:17:28,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,579] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,579] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa55ba1c-ce39-4b02-8e3b-4a09767d87f1/GCF_003012705.1_ASM301270v1_genomic.fna.gz | prodigal -d GCF_003012705.1_ASM301270v1_genomic.fna/cds.fna -a GCF_003012705.1_ASM301270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:47,359] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:47,359] [INFO] Task started: HMMsearch
[2024-01-24 13:17:47,359] [INFO] Running command: hmmsearch --tblout GCF_003012705.1_ASM301270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/reference_markers.hmm GCF_003012705.1_ASM301270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:47,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:47,682] [INFO] Found 6/6 markers.
[2024-01-24 13:17:47,734] [INFO] Query marker FASTA was written to GCF_003012705.1_ASM301270v1_genomic.fna/markers.fasta
[2024-01-24 13:17:47,734] [INFO] Task started: Blastn
[2024-01-24 13:17:47,734] [INFO] Running command: blastn -query GCF_003012705.1_ASM301270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/reference_markers.fasta -out GCF_003012705.1_ASM301270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:48,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:48,676] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:48,677] [INFO] Target genome list was writen to GCF_003012705.1_ASM301270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:48,688] [INFO] Task started: fastANI
[2024-01-24 13:17:48,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa55ba1c-ce39-4b02-8e3b-4a09767d87f1/GCF_003012705.1_ASM301270v1_genomic.fna.gz --refList GCF_003012705.1_ASM301270v1_genomic.fna/target_genomes.txt --output GCF_003012705.1_ASM301270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:18,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:18,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:18,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:18,611] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:18,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:18,611] [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	82.0097	955	2051	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	81.2516	858	2051	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	81.1804	833	2051	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.752	882	2051	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	80.7096	791	2051	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	80.6434	899	2051	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	80.638	869	2051	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	80.634	866	2051	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	80.6007	898	2051	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	80.5721	865	2051	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	80.482	855	2051	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	80.466	810	2051	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.4179	901	2051	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	80.3823	872	2051	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.363	803	2051	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	80.3355	924	2051	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	80.3279	892	2051	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	80.3014	819	2051	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.2321	807	2051	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.7399	705	2051	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.6343	737	2051	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.627	738	2051	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.2816	606	2051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:18,613] [INFO] DFAST Taxonomy check result was written to GCF_003012705.1_ASM301270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:18,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:18,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:18,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/checkm_data
[2024-01-24 13:18:18,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:18,673] [INFO] Task started: CheckM
[2024-01-24 13:18:18,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012705.1_ASM301270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012705.1_ASM301270v1_genomic.fna/checkm_input GCF_003012705.1_ASM301270v1_genomic.fna/checkm_result
[2024-01-24 13:19:14,838] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:14,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,855] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:14,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:14,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012705.1_ASM301270v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:14,856] [INFO] Task started: Blastn
[2024-01-24 13:19:14,856] [INFO] Running command: blastn -query GCF_003012705.1_ASM301270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17f7a51a-b53d-446b-8fa7-ea91a10232ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012705.1_ASM301270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:16,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:16,828] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:16,829] [INFO] Target genome list was writen to GCF_003012705.1_ASM301270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:16,872] [INFO] Task started: fastANI
[2024-01-24 13:19:16,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa55ba1c-ce39-4b02-8e3b-4a09767d87f1/GCF_003012705.1_ASM301270v1_genomic.fna.gz --refList GCF_003012705.1_ASM301270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012705.1_ASM301270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:41,052] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:41,067] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:41,068] [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_003012705.1	s__Pseudaminobacter soli	100.0	2051	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874015.1	s__Pseudaminobacter sp017874015	84.3439	1086	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	84.2899	1010	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	82.2812	931	2051	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	82.036	951	2051	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	81.1927	831	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_000372965.1	s__Aminobacter sp000372965	81.0308	896	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952425.1	s__Mesorhizobium sp003952425	80.8658	852	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCF_003289945.1	s__Mesorhizobium hawassense	80.7749	878	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	80.767	830	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791255.1	s__Mesorhizobium sp004791255	80.6899	855	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_016591715.1	s__Mesorhizobium sp016591715	80.6825	882	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727715.1	s__Mesorhizobium terrae	80.5949	873	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	80.5598	781	2051	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	80.4568	812	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	80.4269	843	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004136315.1	s__Mesorhizobium sp004136315	79.7692	795	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.54	97.14	0.95	0.93	3	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	79.2785	607	2051	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_014652835.1	s__Limoniibacter endophyticus	77.0017	197	2051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Limoniibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:41,070] [INFO] GTDB search result was written to GCF_003012705.1_ASM301270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:41,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:41,076] [INFO] DFAST_QC result json was written to GCF_003012705.1_ASM301270v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:41,077] [INFO] DFAST_QC completed!
[2024-01-24 13:19:41,077] [INFO] Total running time: 0h2m14s