[2024-01-24 13:46:02,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:02,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:02,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference
[2024-01-24 13:46:03,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,430] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,430] [INFO] Running command: gunzip -c /var/lib/cwl/stga9e0f386-5a80-40ad-b5ca-f23429654b3f/GCF_014196605.1_ASM1419660v1_genomic.fna.gz | prodigal -d GCF_014196605.1_ASM1419660v1_genomic.fna/cds.fna -a GCF_014196605.1_ASM1419660v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:19,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:19,144] [INFO] Task started: HMMsearch
[2024-01-24 13:46:19,144] [INFO] Running command: hmmsearch --tblout GCF_014196605.1_ASM1419660v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/reference_markers.hmm GCF_014196605.1_ASM1419660v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:19,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:19,476] [INFO] Found 6/6 markers.
[2024-01-24 13:46:19,522] [INFO] Query marker FASTA was written to GCF_014196605.1_ASM1419660v1_genomic.fna/markers.fasta
[2024-01-24 13:46:19,523] [INFO] Task started: Blastn
[2024-01-24 13:46:19,523] [INFO] Running command: blastn -query GCF_014196605.1_ASM1419660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/reference_markers.fasta -out GCF_014196605.1_ASM1419660v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:20,398] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:20,402] [INFO] Selected 20 target genomes.
[2024-01-24 13:46:20,403] [INFO] Target genome list was writen to GCF_014196605.1_ASM1419660v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:20,420] [INFO] Task started: fastANI
[2024-01-24 13:46:20,421] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e0f386-5a80-40ad-b5ca-f23429654b3f/GCF_014196605.1_ASM1419660v1_genomic.fna.gz --refList GCF_014196605.1_ASM1419660v1_genomic.fna/target_genomes.txt --output GCF_014196605.1_ASM1419660v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:40,042] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:40,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:40,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:40,058] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:40,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:40,059] [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 rhizoryzae	strain=DSM 29514	GCA_014196605.1	451876	451876	type	True	100.0	1657	1658	95	conclusive
Rhizobium rhizoryzae	strain=DSM 29514	GCA_011046895.1	451876	451876	type	True	99.9574	1628	1658	95	conclusive
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	80.3079	783	1658	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.6024	533	1658	95	below_threshold
Agrobacterium larrymoorei	strain=CFBP5473	GCA_005145045.1	160699	160699	type	True	78.5789	425	1658	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	78.5682	403	1658	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	78.5273	494	1658	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	78.5129	392	1658	95	below_threshold
Agrobacterium larrymoorei	strain=ATCC 51759	GCA_000518585.1	160699	160699	type	True	78.5124	416	1658	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.4447	480	1658	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	78.3996	419	1658	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.3631	481	1658	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	78.3348	437	1658	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.2595	404	1658	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.2416	398	1658	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.1989	516	1658	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	78.1919	382	1658	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.1619	381	1658	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.1	456	1658	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.9067	387	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:40,061] [INFO] DFAST Taxonomy check result was written to GCF_014196605.1_ASM1419660v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:40,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:40,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:40,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/checkm_data
[2024-01-24 13:46:40,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:40,112] [INFO] Task started: CheckM
[2024-01-24 13:46:40,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196605.1_ASM1419660v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196605.1_ASM1419660v1_genomic.fna/checkm_input GCF_014196605.1_ASM1419660v1_genomic.fna/checkm_result
[2024-01-24 13:47:28,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:28,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:28,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:28,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:28,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196605.1_ASM1419660v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:28,889] [INFO] Task started: Blastn
[2024-01-24 13:47:28,889] [INFO] Running command: blastn -query GCF_014196605.1_ASM1419660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f16e798-014a-497d-aa5a-14f1730943ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196605.1_ASM1419660v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:30,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:30,536] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:30,537] [INFO] Target genome list was writen to GCF_014196605.1_ASM1419660v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:30,544] [INFO] Task started: fastANI
[2024-01-24 13:47:30,544] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e0f386-5a80-40ad-b5ca-f23429654b3f/GCF_014196605.1_ASM1419660v1_genomic.fna.gz --refList GCF_014196605.1_ASM1419660v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196605.1_ASM1419660v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:40,888] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:40,903] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:40,904] [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_011046895.1	s__Rhizobium_A rhizoryzae	99.9574	1628	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	99.45	98.91	0.95	0.91	3	conclusive
GCF_005222835.1	s__Rhizobium_A sp005222835	90.3269	1296	1658	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_011046245.1	s__Rhizobium_A pseudoryzae	80.3057	784	1658	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	80.2654	801	1658	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_007004135.1	s__Rhizobium_A straminoryzae	80.245	755	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_017877135.1	s__Rhizobium_A galegae_A	79.6743	748	1658	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_005222845.1	s__Rhizobium_A sp005222845	79.6554	712	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466005.1	s__Allorhizobium sp900466005	78.262	377	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_001429725.1	s__Rhizobium sp001429725	77.8954	397	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307905.1	s__Allorhizobium sp002307905	77.766	323	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:40,905] [INFO] GTDB search result was written to GCF_014196605.1_ASM1419660v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:40,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:40,910] [INFO] DFAST_QC result json was written to GCF_014196605.1_ASM1419660v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:40,910] [INFO] DFAST_QC completed!
[2024-01-24 13:47:40,910] [INFO] Total running time: 0h1m39s