[2024-01-24 13:55:19,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference
[2024-01-24 13:55:21,263] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,264] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dbf9395-d25c-47ac-8c5e-d7999d36ffce/GCF_014692495.1_ASM1469249v1_genomic.fna.gz | prodigal -d GCF_014692495.1_ASM1469249v1_genomic.fna/cds.fna -a GCF_014692495.1_ASM1469249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:36,445] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:36,445] [INFO] Task started: HMMsearch
[2024-01-24 13:55:36,445] [INFO] Running command: hmmsearch --tblout GCF_014692495.1_ASM1469249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/reference_markers.hmm GCF_014692495.1_ASM1469249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:36,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:36,766] [INFO] Found 6/6 markers.
[2024-01-24 13:55:36,797] [INFO] Query marker FASTA was written to GCF_014692495.1_ASM1469249v1_genomic.fna/markers.fasta
[2024-01-24 13:55:36,797] [INFO] Task started: Blastn
[2024-01-24 13:55:36,797] [INFO] Running command: blastn -query GCF_014692495.1_ASM1469249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/reference_markers.fasta -out GCF_014692495.1_ASM1469249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:37,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:37,431] [INFO] Selected 14 target genomes.
[2024-01-24 13:55:37,432] [INFO] Target genome list was writen to GCF_014692495.1_ASM1469249v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:37,452] [INFO] Task started: fastANI
[2024-01-24 13:55:37,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbf9395-d25c-47ac-8c5e-d7999d36ffce/GCF_014692495.1_ASM1469249v1_genomic.fna.gz --refList GCF_014692495.1_ASM1469249v1_genomic.fna/target_genomes.txt --output GCF_014692495.1_ASM1469249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:50,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:50,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:50,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:50,835] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:50,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:50,835] [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
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	100.0	1232	1237	95	conclusive
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	83.389	762	1237	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	82.5784	755	1237	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	82.2804	625	1237	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	80.8451	502	1237	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	78.3496	205	1237	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	78.176	178	1237	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	78.167	177	1237	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	77.9315	152	1237	95	below_threshold
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	77.5604	161	1237	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.3207	61	1237	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	75.9045	50	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:50,837] [INFO] DFAST Taxonomy check result was written to GCF_014692495.1_ASM1469249v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:50,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:50,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:50,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/checkm_data
[2024-01-24 13:55:50,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:50,885] [INFO] Task started: CheckM
[2024-01-24 13:55:50,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014692495.1_ASM1469249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014692495.1_ASM1469249v1_genomic.fna/checkm_input GCF_014692495.1_ASM1469249v1_genomic.fna/checkm_result
[2024-01-24 13:56:37,527] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:37,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,547] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:37,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:37,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014692495.1_ASM1469249v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:37,549] [INFO] Task started: Blastn
[2024-01-24 13:56:37,549] [INFO] Running command: blastn -query GCF_014692495.1_ASM1469249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a85468-7f01-4920-b296-67fe98635975/dqc_reference/reference_markers_gtdb.fasta -out GCF_014692495.1_ASM1469249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:38,347] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:38,351] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:38,352] [INFO] Target genome list was writen to GCF_014692495.1_ASM1469249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:38,370] [INFO] Task started: fastANI
[2024-01-24 13:56:38,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbf9395-d25c-47ac-8c5e-d7999d36ffce/GCF_014692495.1_ASM1469249v1_genomic.fna.gz --refList GCF_014692495.1_ASM1469249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014692495.1_ASM1469249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:47,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:47,049] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:47,049] [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_011043515.1	s__Sphingobacterium sp011043515	98.841	1064	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	conclusive
GCF_008520265.1	s__Sphingobacterium cavernae	83.4282	761	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	82.6176	751	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	82.2522	629	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342685.1	s__Sphingobacterium alimentarium	80.8159	504	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	79.0218	188	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_014219015.1	s__Sphingobacterium sp002476975	78.7338	181	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCF_016725325.1	s__Sphingobacterium sp002418355	78.596	140	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.65	97.65	0.92	0.92	2	-
GCF_006476045.1	s__Sphingobacterium lumbrici	78.5639	179	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168125.1	s__Sphingobacterium nematocida	78.3607	206	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610355.1	s__Sphingobacterium detergens	77.9604	150	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:47,051] [INFO] GTDB search result was written to GCF_014692495.1_ASM1469249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:47,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:47,054] [INFO] DFAST_QC result json was written to GCF_014692495.1_ASM1469249v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:47,054] [INFO] DFAST_QC completed!
[2024-01-24 13:56:47,054] [INFO] Total running time: 0h1m27s