[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference
[2024-01-24 12:00:39,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,377] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1be5a37-4162-41e5-9287-504d09cdfcc5/GCF_014644335.1_ASM1464433v1_genomic.fna.gz | prodigal -d GCF_014644335.1_ASM1464433v1_genomic.fna/cds.fna -a GCF_014644335.1_ASM1464433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:56,953] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:56,954] [INFO] Task started: HMMsearch
[2024-01-24 12:00:56,954] [INFO] Running command: hmmsearch --tblout GCF_014644335.1_ASM1464433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/reference_markers.hmm GCF_014644335.1_ASM1464433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:57,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:57,233] [INFO] Found 6/6 markers.
[2024-01-24 12:00:57,277] [INFO] Query marker FASTA was written to GCF_014644335.1_ASM1464433v1_genomic.fna/markers.fasta
[2024-01-24 12:00:57,278] [INFO] Task started: Blastn
[2024-01-24 12:00:57,278] [INFO] Running command: blastn -query GCF_014644335.1_ASM1464433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/reference_markers.fasta -out GCF_014644335.1_ASM1464433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:57,878] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:57,882] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:57,882] [INFO] Target genome list was writen to GCF_014644335.1_ASM1464433v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:57,886] [INFO] Task started: fastANI
[2024-01-24 12:00:57,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1be5a37-4162-41e5-9287-504d09cdfcc5/GCF_014644335.1_ASM1464433v1_genomic.fna.gz --refList GCF_014644335.1_ASM1464433v1_genomic.fna/target_genomes.txt --output GCF_014644335.1_ASM1464433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:04,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:04,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:04,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:04,991] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:01:04,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:04,991] [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 soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	100.0	1462	1463	95	conclusive
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	99.9954	1461	1463	95	conclusive
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	82.3721	860	1463	95	below_threshold
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	82.3647	867	1463	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	82.3579	862	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:04,993] [INFO] DFAST Taxonomy check result was written to GCF_014644335.1_ASM1464433v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:04,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:04,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:04,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/checkm_data
[2024-01-24 12:01:04,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:05,040] [INFO] Task started: CheckM
[2024-01-24 12:01:05,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644335.1_ASM1464433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644335.1_ASM1464433v1_genomic.fna/checkm_input GCF_014644335.1_ASM1464433v1_genomic.fna/checkm_result
[2024-01-24 12:01:57,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:57,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:57,687] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:57,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:57,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644335.1_ASM1464433v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:57,688] [INFO] Task started: Blastn
[2024-01-24 12:01:57,688] [INFO] Running command: blastn -query GCF_014644335.1_ASM1464433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01910488-dee5-498d-8381-e5c069d98e0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644335.1_ASM1464433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:58,473] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:58,478] [INFO] Selected 11 target genomes.
[2024-01-24 12:01:58,478] [INFO] Target genome list was writen to GCF_014644335.1_ASM1464433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:58,488] [INFO] Task started: fastANI
[2024-01-24 12:01:58,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1be5a37-4162-41e5-9287-504d09cdfcc5/GCF_014644335.1_ASM1464433v1_genomic.fna.gz --refList GCF_014644335.1_ASM1464433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644335.1_ASM1464433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:07,990] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:08,004] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:08,004] [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
GCA_002245855.1	s__Sphingobacterium cellulitidis	97.9542	1319	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	conclusive
GCF_900187125.1	s__Sphingobacterium mizutaii	82.381	859	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCF_014219015.1	s__Sphingobacterium sp002476975	82.0073	856	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCF_009733535.1	s__Sphingobacterium endophyticum	80.9479	702	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901472535.1	s__Sphingobacterium daejeonense	80.5426	686	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.25	97.25	0.90	0.90	2	-
GCF_011046555.1	s__Sphingobacterium lactis	79.2691	379	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009768885.1	s__Sphingobacterium humi	78.8333	299	1463	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	78.6395	179	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_007830445.1	s__Sphingobacterium siyangense	77.9567	159	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
GCF_002000245.1	s__Sphingobacterium sp002000245	77.6253	144	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054045.1	s__Sphingobacterium faecium	77.5073	154	1463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.76	97.52	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:08,006] [INFO] GTDB search result was written to GCF_014644335.1_ASM1464433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:08,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:08,011] [INFO] DFAST_QC result json was written to GCF_014644335.1_ASM1464433v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:08,011] [INFO] DFAST_QC completed!
[2024-01-24 12:02:08,011] [INFO] Total running time: 0h1m31s