[2024-01-24 14:19:02,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference
[2024-01-24 14:19:03,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,861] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e28664c-3cb4-4169-974a-be1fab5e84ea/GCF_004912145.1_ASM491214v1_genomic.fna.gz | prodigal -d GCF_004912145.1_ASM491214v1_genomic.fna/cds.fna -a GCF_004912145.1_ASM491214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:19,644] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:19,644] [INFO] Task started: HMMsearch
[2024-01-24 14:19:19,644] [INFO] Running command: hmmsearch --tblout GCF_004912145.1_ASM491214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/reference_markers.hmm GCF_004912145.1_ASM491214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:19,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:20,000] [INFO] Found 6/6 markers.
[2024-01-24 14:19:20,045] [INFO] Query marker FASTA was written to GCF_004912145.1_ASM491214v1_genomic.fna/markers.fasta
[2024-01-24 14:19:20,045] [INFO] Task started: Blastn
[2024-01-24 14:19:20,045] [INFO] Running command: blastn -query GCF_004912145.1_ASM491214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/reference_markers.fasta -out GCF_004912145.1_ASM491214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:21,153] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:21,157] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:21,157] [INFO] Target genome list was writen to GCF_004912145.1_ASM491214v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:21,164] [INFO] Task started: fastANI
[2024-01-24 14:19:21,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e28664c-3cb4-4169-974a-be1fab5e84ea/GCF_004912145.1_ASM491214v1_genomic.fna.gz --refList GCF_004912145.1_ASM491214v1_genomic.fna/target_genomes.txt --output GCF_004912145.1_ASM491214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:35,118] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:35,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:35,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:35,130] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:35,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:35,130] [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 rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	100.0	1741	1741	95	conclusive
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	85.6638	1186	1741	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	85.6275	1195	1741	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	84.0907	1106	1741	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	83.3035	1076	1741	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	80.0135	706	1741	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.9251	709	1741	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.2386	686	1741	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.0427	602	1741	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.9613	620	1741	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.0653	407	1741	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	78.0096	403	1741	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:35,132] [INFO] DFAST Taxonomy check result was written to GCF_004912145.1_ASM491214v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:35,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:35,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:35,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/checkm_data
[2024-01-24 14:19:35,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:35,210] [INFO] Task started: CheckM
[2024-01-24 14:19:35,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004912145.1_ASM491214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004912145.1_ASM491214v1_genomic.fna/checkm_input GCF_004912145.1_ASM491214v1_genomic.fna/checkm_result
[2024-01-24 14:20:23,535] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:23,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:23,558] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:23,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:23,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004912145.1_ASM491214v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:23,559] [INFO] Task started: Blastn
[2024-01-24 14:20:23,559] [INFO] Running command: blastn -query GCF_004912145.1_ASM491214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c51d1b8-61fb-47a6-8905-536f9b5757f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004912145.1_ASM491214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,584] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,589] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:25,589] [INFO] Target genome list was writen to GCF_004912145.1_ASM491214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:25,602] [INFO] Task started: fastANI
[2024-01-24 14:20:25,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e28664c-3cb4-4169-974a-be1fab5e84ea/GCF_004912145.1_ASM491214v1_genomic.fna.gz --refList GCF_004912145.1_ASM491214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004912145.1_ASM491214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:42,015] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:42,029] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:42,029] [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_004912145.1	s__Allorhizobium rhizophilum	100.0	1741	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	conclusive
GCA_900466945.1	s__Allorhizobium sp900466945	89.3689	1397	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900473745.1	s__Allorhizobium sp900473745	89.2561	1384	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855515.1	s__Allorhizobium sp002855515	87.3844	1274	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156055.1	s__Allorhizobium sp900156055	86.3383	1256	1741	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	86.1234	1258	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCF_000300855.1	s__Allorhizobium albertimagni	85.8381	1305	1741	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	85.6228	1196	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_014237835.1	s__Allorhizobium sp014237835	84.9739	1189	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205195.1	s__Allorhizobium wuzhouense	84.0936	1107	1741	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	83.9938	1078	1741	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	83.7183	1044	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900465605.1	s__Allorhizobium sp900465605	80.0096	696	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:42,031] [INFO] GTDB search result was written to GCF_004912145.1_ASM491214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:42,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:42,037] [INFO] DFAST_QC result json was written to GCF_004912145.1_ASM491214v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:42,038] [INFO] DFAST_QC completed!
[2024-01-24 14:20:42,038] [INFO] Total running time: 0h1m39s