[2024-01-24 11:35:11,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference
[2024-01-24 11:35:12,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,688] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,688] [INFO] Running command: gunzip -c /var/lib/cwl/stgbacc0784-9926-4915-9e82-55662c0d3931/GCF_003337715.1_ASM333771v1_genomic.fna.gz | prodigal -d GCF_003337715.1_ASM333771v1_genomic.fna/cds.fna -a GCF_003337715.1_ASM333771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:25,916] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:25,917] [INFO] Task started: HMMsearch
[2024-01-24 11:35:25,917] [INFO] Running command: hmmsearch --tblout GCF_003337715.1_ASM333771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/reference_markers.hmm GCF_003337715.1_ASM333771v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:26,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:26,192] [INFO] Found 6/6 markers.
[2024-01-24 11:35:26,233] [INFO] Query marker FASTA was written to GCF_003337715.1_ASM333771v1_genomic.fna/markers.fasta
[2024-01-24 11:35:26,233] [INFO] Task started: Blastn
[2024-01-24 11:35:26,233] [INFO] Running command: blastn -query GCF_003337715.1_ASM333771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/reference_markers.fasta -out GCF_003337715.1_ASM333771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:27,277] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:27,281] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:27,281] [INFO] Target genome list was writen to GCF_003337715.1_ASM333771v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:27,287] [INFO] Task started: fastANI
[2024-01-24 11:35:27,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacc0784-9926-4915-9e82-55662c0d3931/GCF_003337715.1_ASM333771v1_genomic.fna.gz --refList GCF_003337715.1_ASM333771v1_genomic.fna/target_genomes.txt --output GCF_003337715.1_ASM333771v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:44,783] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:44,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:44,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:44,796] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:44,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:44,797] [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 lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	100.0	1489	1490	95	conclusive
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	90.9553	1251	1490	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	89.7693	1235	1490	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	81.5689	892	1490	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	80.4888	662	1490	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3126	686	1490	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.2273	719	1490	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	80.1512	724	1490	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	80.0492	735	1490	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	79.7962	566	1490	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.6974	645	1490	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	79.694	642	1490	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.4784	656	1490	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	79.0499	617	1490	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.7064	340	1490	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.6595	337	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:44,798] [INFO] DFAST Taxonomy check result was written to GCF_003337715.1_ASM333771v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:44,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:44,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:44,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/checkm_data
[2024-01-24 11:35:44,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:44,842] [INFO] Task started: CheckM
[2024-01-24 11:35:44,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337715.1_ASM333771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337715.1_ASM333771v1_genomic.fna/checkm_input GCF_003337715.1_ASM333771v1_genomic.fna/checkm_result
[2024-01-24 11:36:25,497] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:25,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:25,517] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:25,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:25,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337715.1_ASM333771v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:25,518] [INFO] Task started: Blastn
[2024-01-24 11:36:25,518] [INFO] Running command: blastn -query GCF_003337715.1_ASM333771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6077851b-e599-4e8d-aa3c-94c8c389bbee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337715.1_ASM333771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:27,634] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:27,638] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:27,638] [INFO] Target genome list was writen to GCF_003337715.1_ASM333771v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:27,646] [INFO] Task started: fastANI
[2024-01-24 11:36:27,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacc0784-9926-4915-9e82-55662c0d3931/GCF_003337715.1_ASM333771v1_genomic.fna.gz --refList GCF_003337715.1_ASM333771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337715.1_ASM333771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:40,094] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:40,111] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:40,112] [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_003337715.1	s__Allorhizobium lividum	100.0	1489	1490	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_900466005.1	s__Allorhizobium sp900466005	94.5321	1301	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCA_900465605.1	s__Allorhizobium sp900465605	91.04	1241	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCF_014126615.1	s__Allorhizobium thiooxidans	89.7741	1234	1490	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	81.5645	892	1490	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	81.2625	829	1490	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	80.9436	790	1490	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	80.6601	773	1490	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	80.4804	663	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198335.1	s__Rhizobium leguminosarum_N	79.5945	653	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.95	99.93	0.95	0.91	10	-
GCF_004341105.1	s__Rhizobium sp004341105	79.0139	539	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.64	99.64	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:40,113] [INFO] GTDB search result was written to GCF_003337715.1_ASM333771v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:40,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:40,120] [INFO] DFAST_QC result json was written to GCF_003337715.1_ASM333771v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:40,120] [INFO] DFAST_QC completed!
[2024-01-24 11:36:40,120] [INFO] Total running time: 0h1m29s