[2024-01-24 12:22:48,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference
[2024-01-24 12:22:49,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,532] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg77e4ae8c-de2a-4d24-bc79-4a91fa21bd6b/GCF_014126615.1_ASM1412661v1_genomic.fna.gz | prodigal -d GCF_014126615.1_ASM1412661v1_genomic.fna/cds.fna -a GCF_014126615.1_ASM1412661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:04,273] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:04,274] [INFO] Task started: HMMsearch
[2024-01-24 12:23:04,274] [INFO] Running command: hmmsearch --tblout GCF_014126615.1_ASM1412661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/reference_markers.hmm GCF_014126615.1_ASM1412661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:04,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:04,539] [INFO] Found 6/6 markers.
[2024-01-24 12:23:04,584] [INFO] Query marker FASTA was written to GCF_014126615.1_ASM1412661v1_genomic.fna/markers.fasta
[2024-01-24 12:23:04,585] [INFO] Task started: Blastn
[2024-01-24 12:23:04,585] [INFO] Running command: blastn -query GCF_014126615.1_ASM1412661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/reference_markers.fasta -out GCF_014126615.1_ASM1412661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:05,741] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:05,746] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:05,746] [INFO] Target genome list was writen to GCF_014126615.1_ASM1412661v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:05,756] [INFO] Task started: fastANI
[2024-01-24 12:23:05,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg77e4ae8c-de2a-4d24-bc79-4a91fa21bd6b/GCF_014126615.1_ASM1412661v1_genomic.fna.gz --refList GCF_014126615.1_ASM1412661v1_genomic.fna/target_genomes.txt --output GCF_014126615.1_ASM1412661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:25,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:25,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:25,119] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:25,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:25,119] [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
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	100.0	1677	1680	95	conclusive
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	90.9676	1425	1680	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	89.7497	1243	1680	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	81.5249	877	1680	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.309	634	1680	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.3078	717	1680	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	80.3025	683	1680	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2803	677	1680	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	80.2515	697	1680	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	80.2046	711	1680	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	79.5969	626	1680	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	79.531	584	1680	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	79.4171	686	1680	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.339	580	1680	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	79.0943	598	1680	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	78.9321	551	1680	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.9311	552	1680	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	78.6935	594	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,121] [INFO] DFAST Taxonomy check result was written to GCF_014126615.1_ASM1412661v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:25,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:25,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:25,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/checkm_data
[2024-01-24 12:23:25,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:25,173] [INFO] Task started: CheckM
[2024-01-24 12:23:25,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014126615.1_ASM1412661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014126615.1_ASM1412661v1_genomic.fna/checkm_input GCF_014126615.1_ASM1412661v1_genomic.fna/checkm_result
[2024-01-24 12:24:08,534] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:08,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:08,558] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:08,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:08,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014126615.1_ASM1412661v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:08,559] [INFO] Task started: Blastn
[2024-01-24 12:24:08,559] [INFO] Running command: blastn -query GCF_014126615.1_ASM1412661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e240e0a-bf49-4316-a034-d32fa881dcc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014126615.1_ASM1412661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:10,657] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:10,661] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:10,661] [INFO] Target genome list was writen to GCF_014126615.1_ASM1412661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:10,668] [INFO] Task started: fastANI
[2024-01-24 12:24:10,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg77e4ae8c-de2a-4d24-bc79-4a91fa21bd6b/GCF_014126615.1_ASM1412661v1_genomic.fna.gz --refList GCF_014126615.1_ASM1412661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014126615.1_ASM1412661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:22,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:22,386] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:22,386] [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_014126615.1	s__Allorhizobium thiooxidans	100.0	1678	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900465605.1	s__Allorhizobium sp900465605	91.0092	1363	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCA_900466005.1	s__Allorhizobium sp900466005	89.905	1402	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_003337715.1	s__Allorhizobium lividum	89.7497	1243	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518785.1	s__Allorhizobium selenitireducens	81.5214	879	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	81.2413	816	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473245.1	s__Allorhizobium sp900473245	80.552	790	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.81	98.34	0.95	0.93	20	-
GCF_002600635.1	s__Allorhizobium sp002600635	80.4696	781	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307905.1	s__Allorhizobium sp002307905	80.3945	649	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	80.28	685	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466475.1	s__Rhizobium sp900466475	79.1089	561	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.15	97.80	0.95	0.94	17	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:22,388] [INFO] GTDB search result was written to GCF_014126615.1_ASM1412661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:22,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:22,392] [INFO] DFAST_QC result json was written to GCF_014126615.1_ASM1412661v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:22,392] [INFO] DFAST_QC completed!
[2024-01-24 12:24:22,392] [INFO] Total running time: 0h1m34s