[2024-01-24 13:21:11,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,156] [INFO] DQC Reference Directory: /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference
[2024-01-24 13:21:12,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,385] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,386] [INFO] Running command: gunzip -c /var/lib/cwl/stg78fc6550-8d74-4b7e-80b2-3ae1c4fefaf1/GCF_009617585.1_ASM961758v1_genomic.fna.gz | prodigal -d GCF_009617585.1_ASM961758v1_genomic.fna/cds.fna -a GCF_009617585.1_ASM961758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:31,267] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:31,268] [INFO] Task started: HMMsearch
[2024-01-24 13:21:31,268] [INFO] Running command: hmmsearch --tblout GCF_009617585.1_ASM961758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/reference_markers.hmm GCF_009617585.1_ASM961758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:31,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:31,598] [INFO] Found 6/6 markers.
[2024-01-24 13:21:31,651] [INFO] Query marker FASTA was written to GCF_009617585.1_ASM961758v1_genomic.fna/markers.fasta
[2024-01-24 13:21:31,651] [INFO] Task started: Blastn
[2024-01-24 13:21:31,651] [INFO] Running command: blastn -query GCF_009617585.1_ASM961758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/reference_markers.fasta -out GCF_009617585.1_ASM961758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:32,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:32,580] [INFO] Selected 23 target genomes.
[2024-01-24 13:21:32,581] [INFO] Target genome list was writen to GCF_009617585.1_ASM961758v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:32,597] [INFO] Task started: fastANI
[2024-01-24 13:21:32,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg78fc6550-8d74-4b7e-80b2-3ae1c4fefaf1/GCF_009617585.1_ASM961758v1_genomic.fna.gz --refList GCF_009617585.1_ASM961758v1_genomic.fna/target_genomes.txt --output GCF_009617585.1_ASM961758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:56,590] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:56,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:56,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:56,608] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:21:56,609] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:21:56,609] [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 wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	81.2376	869	2018	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	81.2172	859	2018	95	below_threshold
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	80.8136	864	2018	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	80.3549	847	2018	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.0928	779	2018	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	80.0069	789	2018	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.3424	713	2018	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.3332	694	2018	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.3274	636	2018	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	79.1869	665	2018	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	79.1823	554	2018	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	79.1493	526	2018	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	79.1455	535	2018	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	79.0975	545	2018	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.0258	644	2018	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.9442	570	2018	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.9213	610	2018	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.8176	639	2018	95	below_threshold
Agrobacterium larrymoorei	strain=CFBP5473	GCA_005145045.1	160699	160699	type	True	78.8161	564	2018	95	below_threshold
Agrobacterium larrymoorei	strain=ATCC 51759	GCA_000518585.1	160699	160699	type	True	78.8064	543	2018	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	78.7769	637	2018	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.5102	480	2018	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4493	486	2018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:56,611] [INFO] DFAST Taxonomy check result was written to GCF_009617585.1_ASM961758v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:56,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:56,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:56,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/checkm_data
[2024-01-24 13:21:56,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:56,676] [INFO] Task started: CheckM
[2024-01-24 13:21:56,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009617585.1_ASM961758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009617585.1_ASM961758v1_genomic.fna/checkm_input GCF_009617585.1_ASM961758v1_genomic.fna/checkm_result
[2024-01-24 13:22:54,819] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:54,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:54,845] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:54,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:54,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009617585.1_ASM961758v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:54,846] [INFO] Task started: Blastn
[2024-01-24 13:22:54,846] [INFO] Running command: blastn -query GCF_009617585.1_ASM961758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge26456d2-ef44-491f-8e69-1b95764fd24d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009617585.1_ASM961758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:56,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:56,550] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:56,550] [INFO] Target genome list was writen to GCF_009617585.1_ASM961758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:56,605] [INFO] Task started: fastANI
[2024-01-24 13:22:56,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg78fc6550-8d74-4b7e-80b2-3ae1c4fefaf1/GCF_009617585.1_ASM961758v1_genomic.fna.gz --refList GCF_009617585.1_ASM961758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009617585.1_ASM961758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:15,434] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:15,453] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:15,454] [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_009617585.1	s__Neorhizobium cerealis	100.0	2017	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004343585.1	s__Neorhizobium sp004343585	86.8653	1423	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472395.1	s__Neorhizobium sp900472395	86.5025	1323	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	81.0945	870	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCA_002376235.1	s__Neorhizobium sp002376235	81.0217	819	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829835.1	s__Neorhizobium sp002431175	80.899	896	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.71	95.71	0.88	0.88	2	-
GCF_006335145.1	s__Neorhizobium smilacinae	80.8138	864	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902167985.1	s__Neorhizobium sp902167985	80.5234	784	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	80.2118	772	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282095.2	s__Neorhizobium sp000282095	80.1477	806	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877135.1	s__Rhizobium_A galegae_A	79.8303	741	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760785.1	s__Rhizobium_A sp018760785	79.8102	726	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855515.1	s__Allorhizobium sp002855515	79.2073	520	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900468805.1	s__Rhizobium sp900468805	78.8096	634	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.10	98.22	0.94	0.90	7	-
GCF_017599385.1	s__Allorhizobium sp017599385	78.5972	466	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.20	97.20	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:15,455] [INFO] GTDB search result was written to GCF_009617585.1_ASM961758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:15,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:15,460] [INFO] DFAST_QC result json was written to GCF_009617585.1_ASM961758v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:15,460] [INFO] DFAST_QC completed!
[2024-01-24 13:23:15,461] [INFO] Total running time: 0h2m4s