[2024-01-24 13:17:41,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference
[2024-01-24 13:17:42,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:42,893] [INFO] Task started: Prodigal
[2024-01-24 13:17:42,893] [INFO] Running command: gunzip -c /var/lib/cwl/stgd80fe777-fc4a-4890-ba0d-2c4787ac6e7b/GCF_007990895.1_ASM799089v1_genomic.fna.gz | prodigal -d GCF_007990895.1_ASM799089v1_genomic.fna/cds.fna -a GCF_007990895.1_ASM799089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:03,199] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:03,200] [INFO] Task started: HMMsearch
[2024-01-24 13:18:03,200] [INFO] Running command: hmmsearch --tblout GCF_007990895.1_ASM799089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/reference_markers.hmm GCF_007990895.1_ASM799089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:03,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:03,509] [INFO] Found 6/6 markers.
[2024-01-24 13:18:03,549] [INFO] Query marker FASTA was written to GCF_007990895.1_ASM799089v1_genomic.fna/markers.fasta
[2024-01-24 13:18:03,550] [INFO] Task started: Blastn
[2024-01-24 13:18:03,550] [INFO] Running command: blastn -query GCF_007990895.1_ASM799089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/reference_markers.fasta -out GCF_007990895.1_ASM799089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:04,160] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:04,164] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:04,165] [INFO] Target genome list was writen to GCF_007990895.1_ASM799089v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:04,243] [INFO] Task started: fastANI
[2024-01-24 13:18:04,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80fe777-fc4a-4890-ba0d-2c4787ac6e7b/GCF_007990895.1_ASM799089v1_genomic.fna.gz --refList GCF_007990895.1_ASM799089v1_genomic.fna/target_genomes.txt --output GCF_007990895.1_ASM799089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:14,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:14,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:14,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:14,120] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:14,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:14,120] [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 mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	100.0	1480	1484	95	conclusive
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	99.9998	1483	1484	95	conclusive
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	99.9994	1482	1484	95	conclusive
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	82.4186	837	1484	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	82.4004	843	1484	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	78.3636	110	1484	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.4794	126	1484	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.6767	51	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:14,122] [INFO] DFAST Taxonomy check result was written to GCF_007990895.1_ASM799089v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:14,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:14,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:14,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/checkm_data
[2024-01-24 13:18:14,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:14,179] [INFO] Task started: CheckM
[2024-01-24 13:18:14,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990895.1_ASM799089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990895.1_ASM799089v1_genomic.fna/checkm_input GCF_007990895.1_ASM799089v1_genomic.fna/checkm_result
[2024-01-24 13:19:12,995] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:12,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:13,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:13,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990895.1_ASM799089v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:13,017] [INFO] Task started: Blastn
[2024-01-24 13:19:13,018] [INFO] Running command: blastn -query GCF_007990895.1_ASM799089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f16b5ec-64f2-4361-8743-1d47d32578e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990895.1_ASM799089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:13,843] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:13,847] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:13,847] [INFO] Target genome list was writen to GCF_007990895.1_ASM799089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:13,942] [INFO] Task started: fastANI
[2024-01-24 13:19:13,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80fe777-fc4a-4890-ba0d-2c4787ac6e7b/GCF_007990895.1_ASM799089v1_genomic.fna.gz --refList GCF_007990895.1_ASM799089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990895.1_ASM799089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:23,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,335] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:23,336] [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_900187125.1	s__Sphingobacterium mizutaii	99.9998	1483	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	conclusive
GCF_014219015.1	s__Sphingobacterium sp002476975	89.1141	1262	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	82.3061	809	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_901472535.1	s__Sphingobacterium daejeonense	81.0739	648	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.25	97.25	0.90	0.90	2	-
GCF_009733535.1	s__Sphingobacterium endophyticum	80.6797	665	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046555.1	s__Sphingobacterium lactis	79.3854	391	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002354335.1	s__Sphingobacterium sp002354335	79.086	276	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	78.1017	137	1484	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	77.8619	136	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627955.1	s__Sphingobacterium puteale	77.4595	135	1484	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 13:19:23,338] [INFO] GTDB search result was written to GCF_007990895.1_ASM799089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:23,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:23,343] [INFO] DFAST_QC result json was written to GCF_007990895.1_ASM799089v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:23,343] [INFO] DFAST_QC completed!
[2024-01-24 13:19:23,343] [INFO] Total running time: 0h1m42s