[2024-01-25 18:42:05,627] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference
[2024-01-25 18:42:06,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,839] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,840] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f6f90e-a257-468e-9fa5-b309fbba3f4b/GCF_003205195.1_ASM320519v1_genomic.fna.gz | prodigal -d GCF_003205195.1_ASM320519v1_genomic.fna/cds.fna -a GCF_003205195.1_ASM320519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:20,140] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:20,140] [INFO] Task started: HMMsearch
[2024-01-25 18:42:20,140] [INFO] Running command: hmmsearch --tblout GCF_003205195.1_ASM320519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/reference_markers.hmm GCF_003205195.1_ASM320519v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:20,423] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:20,424] [INFO] Found 6/6 markers.
[2024-01-25 18:42:20,476] [INFO] Query marker FASTA was written to GCF_003205195.1_ASM320519v1_genomic.fna/markers.fasta
[2024-01-25 18:42:20,476] [INFO] Task started: Blastn
[2024-01-25 18:42:20,476] [INFO] Running command: blastn -query GCF_003205195.1_ASM320519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/reference_markers.fasta -out GCF_003205195.1_ASM320519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:21,444] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:21,448] [INFO] Selected 12 target genomes.
[2024-01-25 18:42:21,448] [INFO] Target genome list was writen to GCF_003205195.1_ASM320519v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:21,452] [INFO] Task started: fastANI
[2024-01-25 18:42:21,453] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f6f90e-a257-468e-9fa5-b309fbba3f4b/GCF_003205195.1_ASM320519v1_genomic.fna.gz --refList GCF_003205195.1_ASM320519v1_genomic.fna/target_genomes.txt --output GCF_003205195.1_ASM320519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:34,413] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:34,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:34,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:34,422] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:34,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:34,422] [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 wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	100.0	1628	1629	95	conclusive
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	85.7687	1206	1629	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	84.1709	1064	1629	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	84.1293	1061	1629	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	84.1122	1107	1629	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	80.1889	713	1629	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	80.0805	734	1629	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.905	726	1629	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.4384	594	1629	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	79.2219	625	1629	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	78.0549	403	1629	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.0291	405	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:34,424] [INFO] DFAST Taxonomy check result was written to GCF_003205195.1_ASM320519v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:34,424] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:34,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:34,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/checkm_data
[2024-01-25 18:42:34,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:34,473] [INFO] Task started: CheckM
[2024-01-25 18:42:34,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003205195.1_ASM320519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003205195.1_ASM320519v1_genomic.fna/checkm_input GCF_003205195.1_ASM320519v1_genomic.fna/checkm_result
[2024-01-25 18:43:17,991] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:17,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:18,009] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:18,010] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:18,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003205195.1_ASM320519v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:18,010] [INFO] Task started: Blastn
[2024-01-25 18:43:18,010] [INFO] Running command: blastn -query GCF_003205195.1_ASM320519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de28410-650f-492f-bd36-c86f9d38388e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003205195.1_ASM320519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:19,848] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:19,851] [INFO] Selected 10 target genomes.
[2024-01-25 18:43:19,851] [INFO] Target genome list was writen to GCF_003205195.1_ASM320519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:19,860] [INFO] Task started: fastANI
[2024-01-25 18:43:19,860] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f6f90e-a257-468e-9fa5-b309fbba3f4b/GCF_003205195.1_ASM320519v1_genomic.fna.gz --refList GCF_003205195.1_ASM320519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003205195.1_ASM320519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:31,889] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:31,896] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:31,896] [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_003205195.1	s__Allorhizobium wuzhouense	100.0	1628	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	conclusive
GCF_001429245.1	s__Allorhizobium sp001429245	86.282	1183	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900473805.1	s__Allorhizobium sp900473805	85.9895	1267	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_006443685.1	s__Allorhizobium glycinendophyticum	85.7781	1205	1629	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	84.429	1111	1629	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	84.1134	1063	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_004912145.1	s__Allorhizobium rhizophilum	84.0993	1108	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
GCA_900473745.1	s__Allorhizobium sp900473745	84.0595	1101	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466945.1	s__Allorhizobium sp900466945	84.0012	1062	1629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000300855.1	s__Allorhizobium albertimagni	83.7852	1073	1629	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 18:43:31,898] [INFO] GTDB search result was written to GCF_003205195.1_ASM320519v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:31,898] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:31,902] [INFO] DFAST_QC result json was written to GCF_003205195.1_ASM320519v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:31,903] [INFO] DFAST_QC completed!
[2024-01-25 18:43:31,903] [INFO] Total running time: 0h1m26s