[2024-01-24 13:10:19,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference
[2024-01-24 13:10:20,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,746] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg48bbdda8-3ff1-4b56-b808-51a678502dae/GCF_021555155.1_ASM2155515v1_genomic.fna.gz | prodigal -d GCF_021555155.1_ASM2155515v1_genomic.fna/cds.fna -a GCF_021555155.1_ASM2155515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:34,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:34,718] [INFO] Task started: HMMsearch
[2024-01-24 13:10:34,718] [INFO] Running command: hmmsearch --tblout GCF_021555155.1_ASM2155515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/reference_markers.hmm GCF_021555155.1_ASM2155515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:35,041] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:35,042] [INFO] Found 6/6 markers.
[2024-01-24 13:10:35,088] [INFO] Query marker FASTA was written to GCF_021555155.1_ASM2155515v1_genomic.fna/markers.fasta
[2024-01-24 13:10:35,088] [INFO] Task started: Blastn
[2024-01-24 13:10:35,089] [INFO] Running command: blastn -query GCF_021555155.1_ASM2155515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/reference_markers.fasta -out GCF_021555155.1_ASM2155515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:36,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:36,256] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:36,257] [INFO] Target genome list was writen to GCF_021555155.1_ASM2155515v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:36,262] [INFO] Task started: fastANI
[2024-01-24 13:10:36,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bbdda8-3ff1-4b56-b808-51a678502dae/GCF_021555155.1_ASM2155515v1_genomic.fna.gz --refList GCF_021555155.1_ASM2155515v1_genomic.fna/target_genomes.txt --output GCF_021555155.1_ASM2155515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:51,731] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:51,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:51,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:51,745] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:51,746] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:51,746] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	83.7836	923	1630	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	83.5206	1067	1630	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	83.4248	1059	1630	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	83.3056	967	1630	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	82.9311	882	1630	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	82.8569	894	1630	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	82.515	965	1630	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	82.3179	881	1630	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	82.2924	882	1630	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	82.1115	956	1630	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	81.999	949	1630	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	81.47	892	1630	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	81.2094	759	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:51,748] [INFO] DFAST Taxonomy check result was written to GCF_021555155.1_ASM2155515v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:51,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:51,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:51,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/checkm_data
[2024-01-24 13:10:51,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:51,805] [INFO] Task started: CheckM
[2024-01-24 13:10:51,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021555155.1_ASM2155515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021555155.1_ASM2155515v1_genomic.fna/checkm_input GCF_021555155.1_ASM2155515v1_genomic.fna/checkm_result
[2024-01-24 13:11:35,370] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:35,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:35,393] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:35,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:35,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021555155.1_ASM2155515v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:35,395] [INFO] Task started: Blastn
[2024-01-24 13:11:35,395] [INFO] Running command: blastn -query GCF_021555155.1_ASM2155515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28862dcd-0d24-4c24-8bbe-5c810a18e860/dqc_reference/reference_markers_gtdb.fasta -out GCF_021555155.1_ASM2155515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:38,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:38,236] [INFO] Selected 18 target genomes.
[2024-01-24 13:11:38,237] [INFO] Target genome list was writen to GCF_021555155.1_ASM2155515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:38,278] [INFO] Task started: fastANI
[2024-01-24 13:11:38,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bbdda8-3ff1-4b56-b808-51a678502dae/GCF_021555155.1_ASM2155515v1_genomic.fna.gz --refList GCF_021555155.1_ASM2155515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021555155.1_ASM2155515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:58,972] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:58,994] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:11:58,995] [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_004341885.1	s__Shinella granuli	83.5078	1068	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_014203155.1	s__Shinella fusca	83.3084	967	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	83.2785	969	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	83.021	932	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	82.8228	898	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	82.5774	982	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_001262505.1	s__Shinella sp001262505	82.525	1016	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_009827055.1	s__Shinella kummerowiae	82.5175	965	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004514435.1	s__Shinella sp004514435	82.2655	885	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCF_003432075.1	s__Shinella sp003432075	82.0707	929	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196765.1	s__Mycoplana azooxidifex	81.9935	950	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046475.1	s__Mycoplana dimorpha	81.8067	802	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220975.1	s__Mycoplana subbaraonis	81.4686	893	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378445.1	s__Mycoplana rhizolycopersici	81.3628	900	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651875.1	s__Sinorhizobium saheli	81.3302	839	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_900155885.1	s__RU20A sp900155885	80.6495	726	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RU20A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429285.1	s__Ensifer sp001429285	80.595	840	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.69	95.18	0.90	0.85	16	-
GCA_900467745.1	s__Rhizobium sp900467745	79.6502	680	1630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.53	95.77	0.88	0.84	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:58,997] [INFO] GTDB search result was written to GCF_021555155.1_ASM2155515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:58,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:59,002] [INFO] DFAST_QC result json was written to GCF_021555155.1_ASM2155515v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:59,003] [INFO] DFAST_QC completed!
[2024-01-24 13:11:59,003] [INFO] Total running time: 0h1m40s