[2024-01-25 19:02:20,402] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference
[2024-01-25 19:02:21,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,523] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg1822530a-fbf7-48f6-a086-ef5574f3a418/GCF_011045115.1_ASM1104511v1_genomic.fna.gz | prodigal -d GCF_011045115.1_ASM1104511v1_genomic.fna/cds.fna -a GCF_011045115.1_ASM1104511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:38,413] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:38,413] [INFO] Task started: HMMsearch
[2024-01-25 19:02:38,413] [INFO] Running command: hmmsearch --tblout GCF_011045115.1_ASM1104511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/reference_markers.hmm GCF_011045115.1_ASM1104511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:38,701] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:38,702] [INFO] Found 6/6 markers.
[2024-01-25 19:02:38,763] [INFO] Query marker FASTA was written to GCF_011045115.1_ASM1104511v1_genomic.fna/markers.fasta
[2024-01-25 19:02:38,763] [INFO] Task started: Blastn
[2024-01-25 19:02:38,763] [INFO] Running command: blastn -query GCF_011045115.1_ASM1104511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/reference_markers.fasta -out GCF_011045115.1_ASM1104511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:39,722] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:39,725] [INFO] Selected 23 target genomes.
[2024-01-25 19:02:39,726] [INFO] Target genome list was writen to GCF_011045115.1_ASM1104511v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:39,741] [INFO] Task started: fastANI
[2024-01-25 19:02:39,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg1822530a-fbf7-48f6-a086-ef5574f3a418/GCF_011045115.1_ASM1104511v1_genomic.fna.gz --refList GCF_011045115.1_ASM1104511v1_genomic.fna/target_genomes.txt --output GCF_011045115.1_ASM1104511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:11,572] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:11,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:11,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:11,586] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:03:11,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:11,587] [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	100.0	2088	2088	95	conclusive
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	81.353	908	2088	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	81.2932	965	2088	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	81.2707	977	2088	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	81.146	989	2088	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	81.1458	978	2088	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	81.1069	1010	2088	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	81.0568	934	2088	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	81.0509	941	2088	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	81.0356	939	2088	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	81.027	979	2088	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	81.0203	909	2088	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	81.0091	939	2088	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	80.9726	905	2088	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	80.957	970	2088	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	80.8991	967	2088	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	80.8913	898	2088	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.8733	943	2088	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.8689	885	2088	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.7254	925	2088	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.5464	741	2088	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.004	681	2088	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0006	680	2088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:11,588] [INFO] DFAST Taxonomy check result was written to GCF_011045115.1_ASM1104511v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:11,589] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:11,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:11,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/checkm_data
[2024-01-25 19:03:11,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:11,649] [INFO] Task started: CheckM
[2024-01-25 19:03:11,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045115.1_ASM1104511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045115.1_ASM1104511v1_genomic.fna/checkm_input GCF_011045115.1_ASM1104511v1_genomic.fna/checkm_result
[2024-01-25 19:03:59,952] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:59,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:59,971] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:59,972] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:59,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045115.1_ASM1104511v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:59,972] [INFO] Task started: Blastn
[2024-01-25 19:03:59,973] [INFO] Running command: blastn -query GCF_011045115.1_ASM1104511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2b7e4e-5ba1-4277-9cc3-fce57332aed9/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045115.1_ASM1104511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:02,002] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:02,005] [INFO] Selected 15 target genomes.
[2024-01-25 19:04:02,005] [INFO] Target genome list was writen to GCF_011045115.1_ASM1104511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:02,029] [INFO] Task started: fastANI
[2024-01-25 19:04:02,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg1822530a-fbf7-48f6-a086-ef5574f3a418/GCF_011045115.1_ASM1104511v1_genomic.fna.gz --refList GCF_011045115.1_ASM1104511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045115.1_ASM1104511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:23,797] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:23,807] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:23,807] [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_011045115.1	s__Pseudaminobacter zhangyensis	100.0	2088	2088	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_003590645.1	s__Pseudaminobacter sp900116595	92.7595	1370	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	82.8942	944	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	81.9143	980	2088	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	81.5933	868	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_016756495.1	s__Mesorhizobium sp016756495	81.1964	1005	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253745.1	s__Mesorhizobium kowhaii	81.1892	1008	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791255.1	s__Mesorhizobium sp004791255	81.1872	945	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	81.1241	1007	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	81.1153	1004	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236565.1	s__Pseudaminobacter alhagi	81.0365	908	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	80.9669	830	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207355.1	s__Mesorhizobium sangaii	80.9572	969	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439515.1	s__Mesorhizobium sp006439515	80.7802	945	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.05	0.91	0.91	2	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	80.7199	925	2088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:23,809] [INFO] GTDB search result was written to GCF_011045115.1_ASM1104511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:23,809] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:23,812] [INFO] DFAST_QC result json was written to GCF_011045115.1_ASM1104511v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:23,813] [INFO] DFAST_QC completed!
[2024-01-25 19:04:23,813] [INFO] Total running time: 0h2m3s