[2023-06-26 21:13:00,352] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:13:00,358] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:13:00,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference
[2023-06-26 21:13:03,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:13:03,316] [INFO] Task started: Prodigal
[2023-06-26 21:13:03,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg13e75a7f-9174-4d01-b807-6f4e9fe711b0/GCA_026126045.1_ASM2612604v1_genomic.fna.gz | prodigal -d GCA_026126045.1_ASM2612604v1_genomic.fna/cds.fna -a GCA_026126045.1_ASM2612604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:13:26,921] [INFO] Task succeeded: Prodigal
[2023-06-26 21:13:26,921] [INFO] Task started: HMMsearch
[2023-06-26 21:13:26,921] [INFO] Running command: hmmsearch --tblout GCA_026126045.1_ASM2612604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/reference_markers.hmm GCA_026126045.1_ASM2612604v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:13:27,317] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:13:27,319] [INFO] Found 6/6 markers.
[2023-06-26 21:13:27,395] [INFO] Query marker FASTA was written to GCA_026126045.1_ASM2612604v1_genomic.fna/markers.fasta
[2023-06-26 21:13:27,396] [INFO] Task started: Blastn
[2023-06-26 21:13:27,396] [INFO] Running command: blastn -query GCA_026126045.1_ASM2612604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/reference_markers.fasta -out GCA_026126045.1_ASM2612604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:13:28,590] [INFO] Task succeeded: Blastn
[2023-06-26 21:13:28,594] [INFO] Selected 9 target genomes.
[2023-06-26 21:13:28,595] [INFO] Target genome list was writen to GCA_026126045.1_ASM2612604v1_genomic.fna/target_genomes.txt
[2023-06-26 21:13:28,596] [INFO] Task started: fastANI
[2023-06-26 21:13:28,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e75a7f-9174-4d01-b807-6f4e9fe711b0/GCA_026126045.1_ASM2612604v1_genomic.fna.gz --refList GCA_026126045.1_ASM2612604v1_genomic.fna/target_genomes.txt --output GCA_026126045.1_ASM2612604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:13:44,392] [INFO] Task succeeded: fastANI
[2023-06-26 21:13:44,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:13:44,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:13:44,407] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-26 21:13:44,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-26 21:13:44,408] [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 yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	98.5347	2079	2562	95	conclusive
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	93.8459	1694	2562	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	88.1859	1245	2562	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	88.1836	1239	2562	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	87.9074	1248	2562	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	86.4679	1386	2562	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	86.0919	1177	2562	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	85.8631	1192	2562	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	85.8013	1179	2562	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:13:44,411] [INFO] DFAST Taxonomy check result was written to GCA_026126045.1_ASM2612604v1_genomic.fna/tc_result.tsv
[2023-06-26 21:13:44,411] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:13:44,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:13:44,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/checkm_data
[2023-06-26 21:13:44,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:13:44,515] [INFO] Task started: CheckM
[2023-06-26 21:13:44,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026126045.1_ASM2612604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026126045.1_ASM2612604v1_genomic.fna/checkm_input GCA_026126045.1_ASM2612604v1_genomic.fna/checkm_result
[2023-06-26 21:14:54,909] [INFO] Task succeeded: CheckM
[2023-06-26 21:14:54,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 21:14:54,939] [INFO] ===== Completeness check finished =====
[2023-06-26 21:14:54,939] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:14:54,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026126045.1_ASM2612604v1_genomic.fna/markers.fasta)
[2023-06-26 21:14:54,941] [INFO] Task started: Blastn
[2023-06-26 21:14:54,941] [INFO] Running command: blastn -query GCA_026126045.1_ASM2612604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7b1c28-0de0-4935-8b0a-653d19f809ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_026126045.1_ASM2612604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:14:57,274] [INFO] Task succeeded: Blastn
[2023-06-26 21:14:57,279] [INFO] Selected 7 target genomes.
[2023-06-26 21:14:57,279] [INFO] Target genome list was writen to GCA_026126045.1_ASM2612604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:14:57,287] [INFO] Task started: fastANI
[2023-06-26 21:14:57,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e75a7f-9174-4d01-b807-6f4e9fe711b0/GCA_026126045.1_ASM2612604v1_genomic.fna.gz --refList GCA_026126045.1_ASM2612604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026126045.1_ASM2612604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:15:09,600] [INFO] Task succeeded: fastANI
[2023-06-26 21:15:09,608] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 21:15:09,608] [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	93.8598	1693	2562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_001262505.1	s__Shinella sp001262505	90.6767	1707	2562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_016839145.1	s__Shinella sp016839145	88.2004	1368	2562	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	88.1949	1238	2562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	87.858	1253	2562	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	87.7614	1316	2562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	77.3307	203	2562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 21:15:09,610] [INFO] GTDB search result was written to GCA_026126045.1_ASM2612604v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:15:09,611] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:15:09,614] [INFO] DFAST_QC result json was written to GCA_026126045.1_ASM2612604v1_genomic.fna/dqc_result.json
[2023-06-26 21:15:09,614] [INFO] DFAST_QC completed!
[2023-06-26 21:15:09,614] [INFO] Total running time: 0h2m9s