[2024-01-25 18:45:05,821] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference
[2024-01-25 18:45:06,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,988] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgdef54579-5156-49ed-a669-7478ea7757f9/GCF_030814435.1_ASM3081443v1_genomic.fna.gz | prodigal -d GCF_030814435.1_ASM3081443v1_genomic.fna/cds.fna -a GCF_030814435.1_ASM3081443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:19,898] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:19,898] [INFO] Task started: HMMsearch
[2024-01-25 18:45:19,898] [INFO] Running command: hmmsearch --tblout GCF_030814435.1_ASM3081443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/reference_markers.hmm GCF_030814435.1_ASM3081443v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:20,172] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:20,173] [INFO] Found 6/6 markers.
[2024-01-25 18:45:20,216] [INFO] Query marker FASTA was written to GCF_030814435.1_ASM3081443v1_genomic.fna/markers.fasta
[2024-01-25 18:45:20,216] [INFO] Task started: Blastn
[2024-01-25 18:45:20,216] [INFO] Running command: blastn -query GCF_030814435.1_ASM3081443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/reference_markers.fasta -out GCF_030814435.1_ASM3081443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:21,054] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:21,058] [INFO] Selected 15 target genomes.
[2024-01-25 18:45:21,059] [INFO] Target genome list was writen to GCF_030814435.1_ASM3081443v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:21,069] [INFO] Task started: fastANI
[2024-01-25 18:45:21,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef54579-5156-49ed-a669-7478ea7757f9/GCF_030814435.1_ASM3081443v1_genomic.fna.gz --refList GCF_030814435.1_ASM3081443v1_genomic.fna/target_genomes.txt --output GCF_030814435.1_ASM3081443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:39,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:39,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:39,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:39,767] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:39,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:39,767] [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
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	85.878	1141	1597	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	85.8181	1128	1597	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	85.7554	1172	1597	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	84.2749	1042	1597	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	83.6536	1001	1597	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.9777	717	1597	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.8625	650	1597	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.5857	645	1597	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.5527	665	1597	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.5113	636	1597	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	79.415	631	1597	95	below_threshold
Rhizobium leucaenae	strain=CFN 299	GCA_014727215.1	29450	29450	type	True	79.1467	530	1597	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	79.1244	580	1597	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	79.095	536	1597	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	78.9215	572	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:39,769] [INFO] DFAST Taxonomy check result was written to GCF_030814435.1_ASM3081443v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:39,770] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:39,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:39,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/checkm_data
[2024-01-25 18:45:39,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:39,817] [INFO] Task started: CheckM
[2024-01-25 18:45:39,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814435.1_ASM3081443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814435.1_ASM3081443v1_genomic.fna/checkm_input GCF_030814435.1_ASM3081443v1_genomic.fna/checkm_result
[2024-01-25 18:46:20,047] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:20,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:20,074] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:20,074] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:20,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814435.1_ASM3081443v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:20,075] [INFO] Task started: Blastn
[2024-01-25 18:46:20,075] [INFO] Running command: blastn -query GCF_030814435.1_ASM3081443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64d6e164-a44a-406c-aba4-3c5211140b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814435.1_ASM3081443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:21,532] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:21,535] [INFO] Selected 14 target genomes.
[2024-01-25 18:46:21,535] [INFO] Target genome list was writen to GCF_030814435.1_ASM3081443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:21,544] [INFO] Task started: fastANI
[2024-01-25 18:46:21,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef54579-5156-49ed-a669-7478ea7757f9/GCF_030814435.1_ASM3081443v1_genomic.fna.gz --refList GCF_030814435.1_ASM3081443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814435.1_ASM3081443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:37,265] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:37,275] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:46:37,275] [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_002855515.1	s__Allorhizobium sp002855515	87.7738	1180	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713475.1	s__Allorhizobium sp001713475	86.4061	1159	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCA_900466945.1	s__Allorhizobium sp900466945	86.1885	1138	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156055.1	s__Allorhizobium sp900156055	86.1308	1147	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237835.1	s__Allorhizobium sp014237835	86.104	1125	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473745.1	s__Allorhizobium sp900473745	86.0762	1153	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806065.1	s__Allorhizobium sp001724035	85.942	1138	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCF_000300855.1	s__Allorhizobium albertimagni	85.8894	1131	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	85.8245	1127	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_003205195.1	s__Allorhizobium wuzhouense	84.2537	1044	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCA_900473805.1	s__Allorhizobium sp900473805	84.2262	1034	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_001429245.1	s__Allorhizobium sp001429245	83.7564	984	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006443685.1	s__Allorhizobium glycinendophyticum	83.6533	1001	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860795.2	s__Allorhizobium desertarenae	81.9292	733	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:37,277] [INFO] GTDB search result was written to GCF_030814435.1_ASM3081443v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:37,277] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:37,280] [INFO] DFAST_QC result json was written to GCF_030814435.1_ASM3081443v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:37,280] [INFO] DFAST_QC completed!
[2024-01-25 18:46:37,280] [INFO] Total running time: 0h1m31s