[2024-01-24 13:01:10,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:10,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:10,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference
[2024-01-24 13:01:11,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:11,352] [INFO] Task started: Prodigal
[2024-01-24 13:01:11,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e81932b-d0c8-4cc9-8468-ea88d75295ec/GCF_020295405.1_ASM2029540v1_genomic.fna.gz | prodigal -d GCF_020295405.1_ASM2029540v1_genomic.fna/cds.fna -a GCF_020295405.1_ASM2029540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:26,480] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:26,481] [INFO] Task started: HMMsearch
[2024-01-24 13:01:26,481] [INFO] Running command: hmmsearch --tblout GCF_020295405.1_ASM2029540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/reference_markers.hmm GCF_020295405.1_ASM2029540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,828] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,865] [INFO] Query marker FASTA was written to GCF_020295405.1_ASM2029540v1_genomic.fna/markers.fasta
[2024-01-24 13:01:26,865] [INFO] Task started: Blastn
[2024-01-24 13:01:26,865] [INFO] Running command: blastn -query GCF_020295405.1_ASM2029540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/reference_markers.fasta -out GCF_020295405.1_ASM2029540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:27,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:27,507] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:27,508] [INFO] Target genome list was writen to GCF_020295405.1_ASM2029540v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:27,514] [INFO] Task started: fastANI
[2024-01-24 13:01:27,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e81932b-d0c8-4cc9-8468-ea88d75295ec/GCF_020295405.1_ASM2029540v1_genomic.fna.gz --refList GCF_020295405.1_ASM2029540v1_genomic.fna/target_genomes.txt --output GCF_020295405.1_ASM2029540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:35,495] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:35,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:35,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:35,504] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:35,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:35,504] [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 bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	80.963	625	1314	95	below_threshold
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	80.9083	606	1314	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	80.8418	554	1314	95	below_threshold
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	80.7243	591	1314	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	80.4871	419	1314	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	78.0693	169	1314	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	78.0253	167	1314	95	below_threshold
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	77.9017	162	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:35,506] [INFO] DFAST Taxonomy check result was written to GCF_020295405.1_ASM2029540v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:35,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:35,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:35,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/checkm_data
[2024-01-24 13:01:35,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:35,550] [INFO] Task started: CheckM
[2024-01-24 13:01:35,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020295405.1_ASM2029540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020295405.1_ASM2029540v1_genomic.fna/checkm_input GCF_020295405.1_ASM2029540v1_genomic.fna/checkm_result
[2024-01-24 13:02:20,623] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:20,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,644] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:20,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:20,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020295405.1_ASM2029540v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:20,645] [INFO] Task started: Blastn
[2024-01-24 13:02:20,645] [INFO] Running command: blastn -query GCF_020295405.1_ASM2029540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f61d96d-c0c8-4417-a861-8c2ecd9a3521/dqc_reference/reference_markers_gtdb.fasta -out GCF_020295405.1_ASM2029540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:21,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:21,440] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:21,440] [INFO] Target genome list was writen to GCF_020295405.1_ASM2029540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:21,478] [INFO] Task started: fastANI
[2024-01-24 13:02:21,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e81932b-d0c8-4cc9-8468-ea88d75295ec/GCF_020295405.1_ASM2029540v1_genomic.fna.gz --refList GCF_020295405.1_ASM2029540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020295405.1_ASM2029540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:32,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:32,394] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:32,394] [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_009829085.1	s__Sphingobacterium bovisgrunnientis	80.9734	624	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_008520265.1	s__Sphingobacterium cavernae	80.9021	607	1314	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	80.8692	550	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	80.7905	571	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_004342685.1	s__Sphingobacterium alimentarium	80.4736	418	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557615.1	s__Sphingobacterium sp009557615	78.5828	155	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006476045.1	s__Sphingobacterium lumbrici	78.4766	168	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354335.1	s__Sphingobacterium sp002354335	78.3802	141	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747525.1	s__Sphingobacterium sp000747525	78.3611	152	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000938735.2	s__Sphingobacterium sp000938735	78.2519	150	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.17	98.17	0.81	0.81	2	-
GCF_003054045.1	s__Sphingobacterium faecium	77.9628	166	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.76	97.52	0.94	0.88	3	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	77.8608	168	1314	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
GCF_001586775.1	s__Sphingobacterium sp001586775	77.7545	92	1314	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 13:02:32,396] [INFO] GTDB search result was written to GCF_020295405.1_ASM2029540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:32,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:32,400] [INFO] DFAST_QC result json was written to GCF_020295405.1_ASM2029540v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:32,400] [INFO] DFAST_QC completed!
[2024-01-24 13:02:32,400] [INFO] Total running time: 0h1m22s