[2024-01-25 18:53:20,514] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:20,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:20,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference
[2024-01-25 18:53:21,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:21,658] [INFO] Task started: Prodigal
[2024-01-25 18:53:21,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg14878047-0b5a-4c85-bce0-2a2421b3ee1c/GCF_009749525.1_ASM974952v1_genomic.fna.gz | prodigal -d GCF_009749525.1_ASM974952v1_genomic.fna/cds.fna -a GCF_009749525.1_ASM974952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:36,134] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:36,135] [INFO] Task started: HMMsearch
[2024-01-25 18:53:36,135] [INFO] Running command: hmmsearch --tblout GCF_009749525.1_ASM974952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/reference_markers.hmm GCF_009749525.1_ASM974952v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:36,471] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:36,472] [INFO] Found 6/6 markers.
[2024-01-25 18:53:36,548] [INFO] Query marker FASTA was written to GCF_009749525.1_ASM974952v1_genomic.fna/markers.fasta
[2024-01-25 18:53:36,548] [INFO] Task started: Blastn
[2024-01-25 18:53:36,548] [INFO] Running command: blastn -query GCF_009749525.1_ASM974952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/reference_markers.fasta -out GCF_009749525.1_ASM974952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:37,546] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:37,549] [INFO] Selected 24 target genomes.
[2024-01-25 18:53:37,549] [INFO] Target genome list was writen to GCF_009749525.1_ASM974952v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:37,584] [INFO] Task started: fastANI
[2024-01-25 18:53:37,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg14878047-0b5a-4c85-bce0-2a2421b3ee1c/GCF_009749525.1_ASM974952v1_genomic.fna.gz --refList GCF_009749525.1_ASM974952v1_genomic.fna/target_genomes.txt --output GCF_009749525.1_ASM974952v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:05,384] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:05,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:05,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:05,398] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:05,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:05,399] [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
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	80.1872	736	1731	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	79.8562	681	1731	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.7418	723	1731	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.7067	747	1731	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.6212	604	1731	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	79.6174	667	1731	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.4841	656	1731	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.375	627	1731	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.3359	671	1731	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	79.3279	682	1731	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	79.2968	638	1731	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	79.1759	691	1731	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	79.1519	697	1731	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	79.1439	670	1731	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	79.1122	693	1731	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.1078	643	1731	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.0858	656	1731	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	79.0493	665	1731	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.9242	522	1731	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	78.9228	639	1731	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.8969	664	1731	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	78.8689	643	1731	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.3152	524	1731	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.3111	524	1731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:05,400] [INFO] DFAST Taxonomy check result was written to GCF_009749525.1_ASM974952v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:05,401] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:05,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:05,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/checkm_data
[2024-01-25 18:54:05,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:05,453] [INFO] Task started: CheckM
[2024-01-25 18:54:05,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009749525.1_ASM974952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009749525.1_ASM974952v1_genomic.fna/checkm_input GCF_009749525.1_ASM974952v1_genomic.fna/checkm_result
[2024-01-25 18:54:50,679] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:50,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:50,701] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:50,701] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:50,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009749525.1_ASM974952v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:50,701] [INFO] Task started: Blastn
[2024-01-25 18:54:50,701] [INFO] Running command: blastn -query GCF_009749525.1_ASM974952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c39919-b39d-47ab-bc6d-8aa500055cf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009749525.1_ASM974952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:52,703] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:52,706] [INFO] Selected 18 target genomes.
[2024-01-25 18:54:52,706] [INFO] Target genome list was writen to GCF_009749525.1_ASM974952v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:52,720] [INFO] Task started: fastANI
[2024-01-25 18:54:52,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg14878047-0b5a-4c85-bce0-2a2421b3ee1c/GCF_009749525.1_ASM974952v1_genomic.fna.gz --refList GCF_009749525.1_ASM974952v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009749525.1_ASM974952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:12,580] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:12,591] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:12,592] [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_009749525.1	s__Im94 sp009749525	100.0	1729	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003015025.1	s__Nitratireductor_D sp003015025	80.1031	746	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	79.9831	739	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.9016	530	1731	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_001050155.1	s__Nitratireductor soli	79.867	680	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	79.8016	696	1731	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_009742725.1	s__Nitratireductor_D arenosus	79.7418	723	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	79.626	606	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	79.6091	667	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	79.444	595	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	79.4282	652	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCA_000824785.1	s__Mesorhizobium plurifarium	79.2993	684	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCF_007830515.1	s__Mesorhizobium tianshanense	79.2376	682	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	79.2175	350	1731	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_016591715.1	s__Mesorhizobium sp016591715	79.2056	675	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	79.1139	643	1731	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_001896885.1	s__65-79 sp001896885	79.0089	565	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__65-79	95.0	99.97	99.97	0.97	0.97	2	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	78.8317	602	1731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:12,593] [INFO] GTDB search result was written to GCF_009749525.1_ASM974952v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:12,593] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:12,597] [INFO] DFAST_QC result json was written to GCF_009749525.1_ASM974952v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:12,597] [INFO] DFAST_QC completed!
[2024-01-25 18:55:12,597] [INFO] Total running time: 0h1m52s