[2024-01-24 11:26:54,315] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg89c0ef36-06a3-4560-b7d9-428243957c95/GCF_902502825.2_E03_1.v3_genomic.fna.gz | prodigal -d GCF_902502825.2_E03_1.v3_genomic.fna/cds.fna -a GCF_902502825.2_E03_1.v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:12,520] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:12,521] [INFO] Task started: HMMsearch
[2024-01-24 11:27:12,521] [INFO] Running command: hmmsearch --tblout GCF_902502825.2_E03_1.v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/reference_markers.hmm GCF_902502825.2_E03_1.v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:12,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:12,800] [INFO] Found 6/6 markers.
[2024-01-24 11:27:12,840] [INFO] Query marker FASTA was written to GCF_902502825.2_E03_1.v3_genomic.fna/markers.fasta
[2024-01-24 11:27:12,841] [INFO] Task started: Blastn
[2024-01-24 11:27:12,841] [INFO] Running command: blastn -query GCF_902502825.2_E03_1.v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/reference_markers.fasta -out GCF_902502825.2_E03_1.v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:13,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:13,854] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:13,854] [INFO] Target genome list was writen to GCF_902502825.2_E03_1.v3_genomic.fna/target_genomes.txt
[2024-01-24 11:27:13,859] [INFO] Task started: fastANI
[2024-01-24 11:27:13,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg89c0ef36-06a3-4560-b7d9-428243957c95/GCF_902502825.2_E03_1.v3_genomic.fna.gz --refList GCF_902502825.2_E03_1.v3_genomic.fna/target_genomes.txt --output GCF_902502825.2_E03_1.v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:24,840] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:24,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:24,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:24,851] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:27:24,851] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:24,852] [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
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	100.0	1578	1579	95	inconclusive
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	99.9603	1513	1579	95	inconclusive
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	99.9258	1523	1579	95	inconclusive
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	95.9686	1254	1579	95	inconclusive
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	95.2953	1215	1579	95	inconclusive
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.7215	534	1579	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.6151	592	1579	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.5945	564	1579	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.3455	524	1579	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.7515	485	1579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,854] [INFO] DFAST Taxonomy check result was written to GCF_902502825.2_E03_1.v3_genomic.fna/tc_result.tsv
[2024-01-24 11:27:24,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:24,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:24,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/checkm_data
[2024-01-24 11:27:24,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:24,900] [INFO] Task started: CheckM
[2024-01-24 11:27:24,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902502825.2_E03_1.v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902502825.2_E03_1.v3_genomic.fna/checkm_input GCF_902502825.2_E03_1.v3_genomic.fna/checkm_result
[2024-01-24 11:28:07,958] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:07,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,982] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:07,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:07,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902502825.2_E03_1.v3_genomic.fna/markers.fasta)
[2024-01-24 11:28:07,983] [INFO] Task started: Blastn
[2024-01-24 11:28:07,983] [INFO] Running command: blastn -query GCF_902502825.2_E03_1.v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb56b6f8d-2711-4d41-bd85-d790e42b274d/dqc_reference/reference_markers_gtdb.fasta -out GCF_902502825.2_E03_1.v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:10,068] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:10,071] [INFO] Selected 17 target genomes.
[2024-01-24 11:28:10,072] [INFO] Target genome list was writen to GCF_902502825.2_E03_1.v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:10,084] [INFO] Task started: fastANI
[2024-01-24 11:28:10,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg89c0ef36-06a3-4560-b7d9-428243957c95/GCF_902502825.2_E03_1.v3_genomic.fna.gz --refList GCF_902502825.2_E03_1.v3_genomic.fna/target_genomes_gtdb.txt --output GCF_902502825.2_E03_1.v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:27,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:27,800] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:27,800] [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_902502825.2	s__Pseudorhizobium flavum	100.0	1577	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	conclusive
GCF_902153245.2	s__Pseudorhizobium endolithicum	83.4662	948	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	98.09	98.09	0.93	0.93	2	-
GCA_000722615.1	s__Pseudorhizobium pelagicum	81.2965	857	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	-
GCF_900177415.1	s__Neorhizobium oryzae_A	80.5382	730	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	79.9307	623	1579	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_000732195.1	s__Neorhizobium vignae	79.8988	689	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731315.1	s__Neorhizobium galegae	79.8902	702	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.31	95.05	0.87	0.81	4	-
GCF_017877055.1	s__Neorhizobium galegae_D	79.8653	706	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760785.1	s__Rhizobium_A sp018760785	79.8346	646	1579	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_002968635.1	s__Neorhizobium alkalisoli	79.7835	628	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111905.1	s__Neorhizobium sp900111905	79.6368	649	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	79.575	620	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCA_900469955.1	s__Neorhizobium sp900469955	79.5532	650	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	79.5464	527	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	79.5268	586	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCA_900465605.1	s__Allorhizobium sp900465605	79.3877	505	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCF_014197145.1	s__Gellertiella hungarica	79.2233	441	1579	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Gellertiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:27,802] [INFO] GTDB search result was written to GCF_902502825.2_E03_1.v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:27,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:27,806] [INFO] DFAST_QC result json was written to GCF_902502825.2_E03_1.v3_genomic.fna/dqc_result.json
[2024-01-24 11:28:27,806] [INFO] DFAST_QC completed!
[2024-01-24 11:28:27,806] [INFO] Total running time: 0h1m33s