[2024-01-24 13:21:47,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference
[2024-01-24 13:21:48,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,422] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg700eca3a-e028-4945-90ae-9121a4a8edcb/GCF_009601405.1_ASM960140v1_genomic.fna.gz | prodigal -d GCF_009601405.1_ASM960140v1_genomic.fna/cds.fna -a GCF_009601405.1_ASM960140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,218] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,218] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,218] [INFO] Running command: hmmsearch --tblout GCF_009601405.1_ASM960140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/reference_markers.hmm GCF_009601405.1_ASM960140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,666] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,744] [INFO] Query marker FASTA was written to GCF_009601405.1_ASM960140v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,745] [INFO] Task started: Blastn
[2024-01-24 13:22:09,745] [INFO] Running command: blastn -query GCF_009601405.1_ASM960140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/reference_markers.fasta -out GCF_009601405.1_ASM960140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,899] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,902] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:10,903] [INFO] Target genome list was writen to GCF_009601405.1_ASM960140v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,904] [INFO] Task started: fastANI
[2024-01-24 13:22:10,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg700eca3a-e028-4945-90ae-9121a4a8edcb/GCF_009601405.1_ASM960140v1_genomic.fna.gz --refList GCF_009601405.1_ASM960140v1_genomic.fna/target_genomes.txt --output GCF_009601405.1_ASM960140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:30,333] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:30,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:30,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:30,345] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:30,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:30,346] [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
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	100.0	2233	2256	95	conclusive
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	99.9369	2057	2256	95	conclusive
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	99.9232	2008	2256	95	conclusive
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	84.7613	1331	2256	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	84.3349	1267	2256	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	83.1707	1277	2256	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	83.126	1299	2256	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	83.0807	1351	2256	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	82.9163	1266	2256	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.952	799	2256	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.9098	879	2256	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.7112	753	2256	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.3528	738	2256	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.391	671	2256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:30,348] [INFO] DFAST Taxonomy check result was written to GCF_009601405.1_ASM960140v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:30,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:30,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:30,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/checkm_data
[2024-01-24 13:22:30,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:30,415] [INFO] Task started: CheckM
[2024-01-24 13:22:30,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009601405.1_ASM960140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009601405.1_ASM960140v1_genomic.fna/checkm_input GCF_009601405.1_ASM960140v1_genomic.fna/checkm_result
[2024-01-24 13:23:29,445] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:29,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:29,475] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:29,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:29,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009601405.1_ASM960140v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:29,476] [INFO] Task started: Blastn
[2024-01-24 13:23:29,476] [INFO] Running command: blastn -query GCF_009601405.1_ASM960140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdba13316-04e5-4478-be34-3e37cc657951/dqc_reference/reference_markers_gtdb.fasta -out GCF_009601405.1_ASM960140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:31,798] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:31,801] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:31,801] [INFO] Target genome list was writen to GCF_009601405.1_ASM960140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:31,802] [INFO] Task started: fastANI
[2024-01-24 13:23:31,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg700eca3a-e028-4945-90ae-9121a4a8edcb/GCF_009601405.1_ASM960140v1_genomic.fna.gz --refList GCF_009601405.1_ASM960140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009601405.1_ASM960140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:44,345] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:44,355] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:44,355] [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_001461695.1	s__Sinorhizobium fredii	99.9369	2057	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	conclusive
GCF_000018545.1	s__Sinorhizobium fredii_A	92.2189	1742	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265205.3	s__Sinorhizobium fredii_B	90.3771	1732	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.03	98.03	0.83	0.83	2	-
GCF_001651865.1	s__Sinorhizobium glycinis	90.3258	1569	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704765.1	s__Sinorhizobium shofinae	89.7633	1416	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378985.1	s__Sinorhizobium sp000378985	88.235	1609	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651855.1	s__Sinorhizobium americanum	88.1854	1556	2256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.81	98.12	0.92	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:44,357] [INFO] GTDB search result was written to GCF_009601405.1_ASM960140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:44,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:44,363] [INFO] DFAST_QC result json was written to GCF_009601405.1_ASM960140v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:44,363] [INFO] DFAST_QC completed!
[2024-01-24 13:23:44,364] [INFO] Total running time: 0h1m57s