[2024-01-24 13:17:14,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference
[2024-01-24 13:17:16,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,303] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg46a662df-3116-454d-99a7-4e15fa28283f/GCF_011045125.1_ASM1104512v1_genomic.fna.gz | prodigal -d GCF_011045125.1_ASM1104512v1_genomic.fna/cds.fna -a GCF_011045125.1_ASM1104512v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:36,949] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:36,949] [INFO] Task started: HMMsearch
[2024-01-24 13:17:36,949] [INFO] Running command: hmmsearch --tblout GCF_011045125.1_ASM1104512v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/reference_markers.hmm GCF_011045125.1_ASM1104512v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:37,295] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:37,297] [INFO] Found 6/6 markers.
[2024-01-24 13:17:37,365] [INFO] Query marker FASTA was written to GCF_011045125.1_ASM1104512v1_genomic.fna/markers.fasta
[2024-01-24 13:17:37,365] [INFO] Task started: Blastn
[2024-01-24 13:17:37,365] [INFO] Running command: blastn -query GCF_011045125.1_ASM1104512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/reference_markers.fasta -out GCF_011045125.1_ASM1104512v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:38,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:38,362] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:38,363] [INFO] Target genome list was writen to GCF_011045125.1_ASM1104512v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:38,366] [INFO] Task started: fastANI
[2024-01-24 13:17:38,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a662df-3116-454d-99a7-4e15fa28283f/GCF_011045125.1_ASM1104512v1_genomic.fna.gz --refList GCF_011045125.1_ASM1104512v1_genomic.fna/target_genomes.txt --output GCF_011045125.1_ASM1104512v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:04,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:04,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:04,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:04,583] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:04,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:04,584] [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 camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	100.0	2265	2279	95	conclusive
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	91.3138	1464	2279	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	81.2676	976	2279	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	81.2243	1004	2279	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	81.2068	1044	2279	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	81.1404	1004	2279	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	80.9865	1026	2279	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	80.9082	985	2279	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.8342	982	2279	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	80.8011	1004	2279	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.7701	985	2279	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	80.6472	1015	2279	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.5357	894	2279	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	80.3775	789	2279	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	80.3434	808	2279	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.3307	793	2279	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.5856	768	2279	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2595	705	2279	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2517	705	2279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:04,586] [INFO] DFAST Taxonomy check result was written to GCF_011045125.1_ASM1104512v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:04,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:04,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:04,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/checkm_data
[2024-01-24 13:18:04,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:04,656] [INFO] Task started: CheckM
[2024-01-24 13:18:04,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045125.1_ASM1104512v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045125.1_ASM1104512v1_genomic.fna/checkm_input GCF_011045125.1_ASM1104512v1_genomic.fna/checkm_result
[2024-01-24 13:19:02,666] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:02,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:02,686] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:02,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:02,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045125.1_ASM1104512v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:02,688] [INFO] Task started: Blastn
[2024-01-24 13:19:02,688] [INFO] Running command: blastn -query GCF_011045125.1_ASM1104512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f8a341-fa0b-41fb-bc44-d6429d7ccd32/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045125.1_ASM1104512v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,674] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:04,674] [INFO] Target genome list was writen to GCF_011045125.1_ASM1104512v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:04,739] [INFO] Task started: fastANI
[2024-01-24 13:19:04,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a662df-3116-454d-99a7-4e15fa28283f/GCF_011045125.1_ASM1104512v1_genomic.fna.gz --refList GCF_011045125.1_ASM1104512v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045125.1_ASM1104512v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:34,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:34,472] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:34,472] [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_011045125.1	s__Pseudaminobacter camelthorni	100.0	2265	2279	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_000236565.1	s__Pseudaminobacter alhagi	91.308	1464	2279	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	81.279	922	2279	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	81.2514	978	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099905.1	s__Mesorhizobium muleiense	81.2374	1002	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_900156895.1	s__Mesorhizobium prunaredense	81.2337	1019	2279	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	81.142	1021	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_016836705.1	s__Mesorhizobium caraganae	81.1299	1007	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	81.0153	812	2279	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	80.9875	969	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952485.1	s__Mesorhizobium sp003952485	80.9605	1014	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_014189435.1	s__Mesorhizobium loti_G	80.9465	1012	2279	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	80.8221	1000	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	80.8188	984	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007003975.1	s__Mesorhizobium sp007003975	80.6979	972	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004801285.1	s__Mesorhizobium composti	80.3773	788	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	80.1031	586	2279	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_016742175.1	s__Aliihoeflea sp016742175	79.7734	627	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.7652	760	2279	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_001427385.1	s__Mesorhizobium sp001427385	79.4741	657	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	79.3623	658	2279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:34,474] [INFO] GTDB search result was written to GCF_011045125.1_ASM1104512v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:34,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:34,479] [INFO] DFAST_QC result json was written to GCF_011045125.1_ASM1104512v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:34,480] [INFO] DFAST_QC completed!
[2024-01-24 13:19:34,480] [INFO] Total running time: 0h2m20s