[2024-01-24 13:23:10,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,560] [INFO] DQC Reference Directory: /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference
[2024-01-24 13:23:11,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:11,848] [INFO] Task started: Prodigal
[2024-01-24 13:23:11,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg909b4449-14f1-4b9e-a90e-44d30cbe4cf0/GCF_014595955.1_ASM1459595v1_genomic.fna.gz | prodigal -d GCF_014595955.1_ASM1459595v1_genomic.fna/cds.fna -a GCF_014595955.1_ASM1459595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:29,325] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:29,326] [INFO] Task started: HMMsearch
[2024-01-24 13:23:29,326] [INFO] Running command: hmmsearch --tblout GCF_014595955.1_ASM1459595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/reference_markers.hmm GCF_014595955.1_ASM1459595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:29,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:29,612] [INFO] Found 6/6 markers.
[2024-01-24 13:23:29,658] [INFO] Query marker FASTA was written to GCF_014595955.1_ASM1459595v1_genomic.fna/markers.fasta
[2024-01-24 13:23:29,658] [INFO] Task started: Blastn
[2024-01-24 13:23:29,658] [INFO] Running command: blastn -query GCF_014595955.1_ASM1459595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/reference_markers.fasta -out GCF_014595955.1_ASM1459595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:30,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:30,675] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:30,676] [INFO] Target genome list was writen to GCF_014595955.1_ASM1459595v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:30,678] [INFO] Task started: fastANI
[2024-01-24 13:23:30,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg909b4449-14f1-4b9e-a90e-44d30cbe4cf0/GCF_014595955.1_ASM1459595v1_genomic.fna.gz --refList GCF_014595955.1_ASM1459595v1_genomic.fna/target_genomes.txt --output GCF_014595955.1_ASM1459595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:52,219] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:52,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:52,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:52,235] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:52,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:52,236] [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
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	100.0	2006	2011	95	conclusive
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	100.0	2006	2011	95	conclusive
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	79.5724	675	2011	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	79.4279	671	2011	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	79.3952	684	2011	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	79.3884	635	2011	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	79.3612	732	2011	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	79.3252	725	2011	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.3054	748	2011	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.1901	646	2011	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	79.1871	658	2011	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	79.0898	665	2011	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.0852	712	2011	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	79.0107	699	2011	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	78.9871	683	2011	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	78.8861	699	2011	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.8525	464	2011	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.5098	520	2011	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	78.3627	440	2011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:52,237] [INFO] DFAST Taxonomy check result was written to GCF_014595955.1_ASM1459595v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:52,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:52,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:52,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/checkm_data
[2024-01-24 13:23:52,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:52,296] [INFO] Task started: CheckM
[2024-01-24 13:23:52,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014595955.1_ASM1459595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014595955.1_ASM1459595v1_genomic.fna/checkm_input GCF_014595955.1_ASM1459595v1_genomic.fna/checkm_result
[2024-01-24 13:24:40,916] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:40,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:40,938] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:40,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:40,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014595955.1_ASM1459595v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:40,939] [INFO] Task started: Blastn
[2024-01-24 13:24:40,939] [INFO] Running command: blastn -query GCF_014595955.1_ASM1459595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb71a3c4b-6be5-442a-b90a-c94d1828f765/dqc_reference/reference_markers_gtdb.fasta -out GCF_014595955.1_ASM1459595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:43,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:43,006] [INFO] Selected 19 target genomes.
[2024-01-24 13:24:43,006] [INFO] Target genome list was writen to GCF_014595955.1_ASM1459595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:43,023] [INFO] Task started: fastANI
[2024-01-24 13:24:43,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg909b4449-14f1-4b9e-a90e-44d30cbe4cf0/GCF_014595955.1_ASM1459595v1_genomic.fna.gz --refList GCF_014595955.1_ASM1459595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014595955.1_ASM1459595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:03,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:03,354] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:03,355] [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_014595955.1	s__Mesorhizobium_D sp014595955	100.0	2006	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003012745.1	s__Mesorhizobium_D ephedrae	81.1626	933	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	79.7446	704	2011	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	79.6537	684	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	79.492	753	2011	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	79.4913	597	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.462	617	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.4556	490	2011	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_004801285.1	s__Mesorhizobium composti	79.4272	671	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCA_905339215.1	s__DUSC01 sp008933895	79.3868	619	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	79.3469	749	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873545.1	s__OAS926 sp014873545	79.3151	705	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.2799	625	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	79.2049	655	2011	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_016756615.1	s__DUSC01 sp016756615	79.028	702	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	98.60	98.60	0.90	0.90	2	-
GCF_900099905.1	s__Mesorhizobium muleiense	79.0139	697	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	78.9929	683	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363725.1	s__Mesorhizobium defluvii	78.8432	465	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	-
GCF_014201615.1	s__Mesorhizobium lusatiense	78.3359	445	2011	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:03,356] [INFO] GTDB search result was written to GCF_014595955.1_ASM1459595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:03,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:03,361] [INFO] DFAST_QC result json was written to GCF_014595955.1_ASM1459595v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:03,362] [INFO] DFAST_QC completed!
[2024-01-24 13:25:03,362] [INFO] Total running time: 0h1m53s