[2024-01-24 11:43:25,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference
[2024-01-24 11:43:30,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2883a3d-e5ba-4a7d-b1ba-a1409c3a165b/GCF_028548475.1_ASM2854847v1_genomic.fna.gz | prodigal -d GCF_028548475.1_ASM2854847v1_genomic.fna/cds.fna -a GCF_028548475.1_ASM2854847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:40,594] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:40,594] [INFO] Task started: HMMsearch
[2024-01-24 11:43:40,594] [INFO] Running command: hmmsearch --tblout GCF_028548475.1_ASM2854847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/reference_markers.hmm GCF_028548475.1_ASM2854847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:40,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:40,872] [INFO] Found 6/6 markers.
[2024-01-24 11:43:40,902] [INFO] Query marker FASTA was written to GCF_028548475.1_ASM2854847v1_genomic.fna/markers.fasta
[2024-01-24 11:43:40,903] [INFO] Task started: Blastn
[2024-01-24 11:43:40,903] [INFO] Running command: blastn -query GCF_028548475.1_ASM2854847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/reference_markers.fasta -out GCF_028548475.1_ASM2854847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:41,924] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:41,930] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:41,931] [INFO] Target genome list was writen to GCF_028548475.1_ASM2854847v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:41,948] [INFO] Task started: fastANI
[2024-01-24 11:43:41,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2883a3d-e5ba-4a7d-b1ba-a1409c3a165b/GCF_028548475.1_ASM2854847v1_genomic.fna.gz --refList GCF_028548475.1_ASM2854847v1_genomic.fna/target_genomes.txt --output GCF_028548475.1_ASM2854847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:53,217] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:53,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:53,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:53,229] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:43:53,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:43:53,230] [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
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	94.2192	970	1101	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	93.8078	965	1101	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	92.4501	859	1101	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	83.4404	753	1101	95	below_threshold
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	82.377	688	1101	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	81.2497	579	1101	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	81.1642	605	1101	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	80.9626	556	1101	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	80.9561	566	1101	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	80.6423	603	1101	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	80.4598	536	1101	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.7887	267	1101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:53,231] [INFO] DFAST Taxonomy check result was written to GCF_028548475.1_ASM2854847v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:53,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:53,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:53,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/checkm_data
[2024-01-24 11:43:53,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:53,270] [INFO] Task started: CheckM
[2024-01-24 11:43:53,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028548475.1_ASM2854847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028548475.1_ASM2854847v1_genomic.fna/checkm_input GCF_028548475.1_ASM2854847v1_genomic.fna/checkm_result
[2024-01-24 11:44:26,545] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:26,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,602] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:26,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:26,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028548475.1_ASM2854847v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:26,603] [INFO] Task started: Blastn
[2024-01-24 11:44:26,604] [INFO] Running command: blastn -query GCF_028548475.1_ASM2854847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaadfba5f-a656-426f-aa1b-0a17112022ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_028548475.1_ASM2854847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:28,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:28,558] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:28,558] [INFO] Target genome list was writen to GCF_028548475.1_ASM2854847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:28,575] [INFO] Task started: fastANI
[2024-01-24 11:44:28,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2883a3d-e5ba-4a7d-b1ba-a1409c3a165b/GCF_028548475.1_ASM2854847v1_genomic.fna.gz --refList GCF_028548475.1_ASM2854847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028548475.1_ASM2854847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:36,670] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:36,682] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:44:36,682] [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_014652475.1	s__Vogesella alkaliphila	94.2392	969	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	93.7879	966	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_014652335.1	s__Vogesella fluminis	92.4503	859	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	84.4553	787	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	83.7723	721	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644045.2	s__Vogesella urethralis	83.447	751	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	82.1508	484	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	81.8267	681	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	81.6671	484	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:36,685] [INFO] GTDB search result was written to GCF_028548475.1_ASM2854847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:36,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:36,689] [INFO] DFAST_QC result json was written to GCF_028548475.1_ASM2854847v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:36,690] [INFO] DFAST_QC completed!
[2024-01-24 11:44:36,690] [INFO] Total running time: 0h1m12s