[2024-01-25 17:48:35,814] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:35,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:35,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference
[2024-01-25 17:48:36,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:36,951] [INFO] Task started: Prodigal
[2024-01-25 17:48:36,952] [INFO] Running command: gunzip -c /var/lib/cwl/stga835134c-1374-443f-b236-4e1d9130e83d/GCF_014652475.1_ASM1465247v1_genomic.fna.gz | prodigal -d GCF_014652475.1_ASM1465247v1_genomic.fna/cds.fna -a GCF_014652475.1_ASM1465247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:46,317] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:46,317] [INFO] Task started: HMMsearch
[2024-01-25 17:48:46,317] [INFO] Running command: hmmsearch --tblout GCF_014652475.1_ASM1465247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/reference_markers.hmm GCF_014652475.1_ASM1465247v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:46,521] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:46,522] [INFO] Found 6/6 markers.
[2024-01-25 17:48:46,547] [INFO] Query marker FASTA was written to GCF_014652475.1_ASM1465247v1_genomic.fna/markers.fasta
[2024-01-25 17:48:46,547] [INFO] Task started: Blastn
[2024-01-25 17:48:46,548] [INFO] Running command: blastn -query GCF_014652475.1_ASM1465247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/reference_markers.fasta -out GCF_014652475.1_ASM1465247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:47,488] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:47,490] [INFO] Selected 13 target genomes.
[2024-01-25 17:48:47,491] [INFO] Target genome list was writen to GCF_014652475.1_ASM1465247v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:47,504] [INFO] Task started: fastANI
[2024-01-25 17:48:47,504] [INFO] Running command: fastANI --query /var/lib/cwl/stga835134c-1374-443f-b236-4e1d9130e83d/GCF_014652475.1_ASM1465247v1_genomic.fna.gz --refList GCF_014652475.1_ASM1465247v1_genomic.fna/target_genomes.txt --output GCF_014652475.1_ASM1465247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:59,980] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:59,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:59,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:59,989] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:59,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:59,989] [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	100.0	1123	1125	95	conclusive
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	94.4532	1018	1125	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	93.9868	859	1125	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	83.7234	761	1125	95	below_threshold
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	82.3586	695	1125	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	81.9876	659	1125	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	81.5926	592	1125	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	81.5763	626	1125	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	81.3159	565	1125	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	81.2582	592	1125	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	81.0324	626	1125	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	80.9114	554	1125	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.8374	355	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:59,991] [INFO] DFAST Taxonomy check result was written to GCF_014652475.1_ASM1465247v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:59,991] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:59,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:59,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/checkm_data
[2024-01-25 17:48:59,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:00,028] [INFO] Task started: CheckM
[2024-01-25 17:49:00,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652475.1_ASM1465247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652475.1_ASM1465247v1_genomic.fna/checkm_input GCF_014652475.1_ASM1465247v1_genomic.fna/checkm_result
[2024-01-25 17:49:30,428] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:30,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:30,453] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:30,453] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:30,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652475.1_ASM1465247v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:30,453] [INFO] Task started: Blastn
[2024-01-25 17:49:30,453] [INFO] Running command: blastn -query GCF_014652475.1_ASM1465247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38ec3642-511c-412c-bd23-a2bf3f48aab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652475.1_ASM1465247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:32,422] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:32,424] [INFO] Selected 9 target genomes.
[2024-01-25 17:49:32,424] [INFO] Target genome list was writen to GCF_014652475.1_ASM1465247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:32,431] [INFO] Task started: fastANI
[2024-01-25 17:49:32,431] [INFO] Running command: fastANI --query /var/lib/cwl/stga835134c-1374-443f-b236-4e1d9130e83d/GCF_014652475.1_ASM1465247v1_genomic.fna.gz --refList GCF_014652475.1_ASM1465247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652475.1_ASM1465247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:40,400] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:40,407] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:40,407] [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	100.0	1123	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003633895.1	s__Vogesella indigofera	94.4532	1018	1125	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	93.9868	859	1125	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	84.7697	799	1125	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	84.0535	742	1125	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	83.7462	758	1125	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	82.4362	485	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	82.0861	497	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	80.898	555	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:40,408] [INFO] GTDB search result was written to GCF_014652475.1_ASM1465247v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:40,409] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:40,412] [INFO] DFAST_QC result json was written to GCF_014652475.1_ASM1465247v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:40,412] [INFO] DFAST_QC completed!
[2024-01-25 17:49:40,412] [INFO] Total running time: 0h1m5s