[2024-01-25 20:23:35,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:35,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:35,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference
[2024-01-25 20:23:36,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:36,771] [INFO] Task started: Prodigal
[2024-01-25 20:23:36,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c168818-c493-4c76-a245-db5ebe1365a1/GCF_002000045.1_ASM200004v1_genomic.fna.gz | prodigal -d GCF_002000045.1_ASM200004v1_genomic.fna/cds.fna -a GCF_002000045.1_ASM200004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:48,933] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:48,933] [INFO] Task started: HMMsearch
[2024-01-25 20:23:48,934] [INFO] Running command: hmmsearch --tblout GCF_002000045.1_ASM200004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/reference_markers.hmm GCF_002000045.1_ASM200004v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:49,218] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:49,219] [INFO] Found 6/6 markers.
[2024-01-25 20:23:49,257] [INFO] Query marker FASTA was written to GCF_002000045.1_ASM200004v1_genomic.fna/markers.fasta
[2024-01-25 20:23:49,257] [INFO] Task started: Blastn
[2024-01-25 20:23:49,257] [INFO] Running command: blastn -query GCF_002000045.1_ASM200004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/reference_markers.fasta -out GCF_002000045.1_ASM200004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:50,222] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:50,225] [INFO] Selected 10 target genomes.
[2024-01-25 20:23:50,226] [INFO] Target genome list was writen to GCF_002000045.1_ASM200004v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:50,264] [INFO] Task started: fastANI
[2024-01-25 20:23:50,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c168818-c493-4c76-a245-db5ebe1365a1/GCF_002000045.1_ASM200004v1_genomic.fna.gz --refList GCF_002000045.1_ASM200004v1_genomic.fna/target_genomes.txt --output GCF_002000045.1_ASM200004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:01,127] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:01,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:01,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:01,138] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 20:24:01,139] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:24:01,139] [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_002000045.1	1335061	1335061	type	True	100.0	1527	1529	95	inconclusive
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	99.9581	1505	1529	95	inconclusive
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	99.9579	1517	1529	95	inconclusive
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	95.9777	1241	1529	95	inconclusive
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	95.2912	1200	1529	95	inconclusive
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.7202	522	1529	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.609	561	1529	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.4775	592	1529	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.3292	512	1529	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.6129	482	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:01,140] [INFO] DFAST Taxonomy check result was written to GCF_002000045.1_ASM200004v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:01,141] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:01,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:01,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/checkm_data
[2024-01-25 20:24:01,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:01,188] [INFO] Task started: CheckM
[2024-01-25 20:24:01,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000045.1_ASM200004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000045.1_ASM200004v1_genomic.fna/checkm_input GCF_002000045.1_ASM200004v1_genomic.fna/checkm_result
[2024-01-25 20:24:37,559] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:37,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:37,580] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:37,580] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:37,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000045.1_ASM200004v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:37,581] [INFO] Task started: Blastn
[2024-01-25 20:24:37,582] [INFO] Running command: blastn -query GCF_002000045.1_ASM200004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd64f39f6-37d3-465d-bba7-2297908da273/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000045.1_ASM200004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:39,545] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:39,548] [INFO] Selected 17 target genomes.
[2024-01-25 20:24:39,548] [INFO] Target genome list was writen to GCF_002000045.1_ASM200004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:39,572] [INFO] Task started: fastANI
[2024-01-25 20:24:39,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c168818-c493-4c76-a245-db5ebe1365a1/GCF_002000045.1_ASM200004v1_genomic.fna.gz --refList GCF_002000045.1_ASM200004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000045.1_ASM200004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:58,068] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:58,079] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:58,079] [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	99.9579	1517	1529	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	83.6409	930	1529	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	81.287	859	1529	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	80.5031	719	1529	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	79.8827	679	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.31	95.05	0.87	0.81	4	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	79.8527	632	1529	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_017877055.1	s__Neorhizobium galegae_D	79.7961	707	1529	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	79.7862	638	1529	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	79.783	706	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	79.6382	558	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_900111905.1	s__Neorhizobium sp900111905	79.6376	631	1529	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	79.619	517	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	79.5833	637	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469955.1	s__Neorhizobium sp900469955	79.5446	648	1529	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	79.5139	621	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCA_900465605.1	s__Allorhizobium sp900465605	79.3355	512	1529	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	79.1252	443	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Gellertiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:58,081] [INFO] GTDB search result was written to GCF_002000045.1_ASM200004v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:58,082] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:58,084] [INFO] DFAST_QC result json was written to GCF_002000045.1_ASM200004v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:58,085] [INFO] DFAST_QC completed!
[2024-01-25 20:24:58,085] [INFO] Total running time: 0h1m22s