[2024-01-25 20:26:05,803] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:05,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:05,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference
[2024-01-25 20:26:06,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:06,965] [INFO] Task started: Prodigal
[2024-01-25 20:26:06,966] [INFO] Running command: gunzip -c /var/lib/cwl/stgd854ccba-ccaa-4cee-abd4-587e85ef6fbf/GCF_030644225.1_ASM3064422v1_genomic.fna.gz | prodigal -d GCF_030644225.1_ASM3064422v1_genomic.fna/cds.fna -a GCF_030644225.1_ASM3064422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:13,639] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:13,639] [INFO] Task started: HMMsearch
[2024-01-25 20:26:13,639] [INFO] Running command: hmmsearch --tblout GCF_030644225.1_ASM3064422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/reference_markers.hmm GCF_030644225.1_ASM3064422v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:13,839] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:13,841] [INFO] Found 6/6 markers.
[2024-01-25 20:26:13,862] [INFO] Query marker FASTA was written to GCF_030644225.1_ASM3064422v1_genomic.fna/markers.fasta
[2024-01-25 20:26:13,863] [INFO] Task started: Blastn
[2024-01-25 20:26:13,863] [INFO] Running command: blastn -query GCF_030644225.1_ASM3064422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/reference_markers.fasta -out GCF_030644225.1_ASM3064422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:14,440] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:14,444] [INFO] Selected 13 target genomes.
[2024-01-25 20:26:14,445] [INFO] Target genome list was writen to GCF_030644225.1_ASM3064422v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:14,453] [INFO] Task started: fastANI
[2024-01-25 20:26:14,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgd854ccba-ccaa-4cee-abd4-587e85ef6fbf/GCF_030644225.1_ASM3064422v1_genomic.fna.gz --refList GCF_030644225.1_ASM3064422v1_genomic.fna/target_genomes.txt --output GCF_030644225.1_ASM3064422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:22,869] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:22,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:22,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:22,875] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:26:22,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:26:22,875] [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
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	86.9852	599	797	95	below_threshold
Selenomonas timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	84.5741	555	797	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	81.684	467	797	95	below_threshold
Selenomonas flueggei	strain=ATCC 43531	GCA_000160695.1	135080	135080	type	True	81.2927	409	797	95	below_threshold
Selenomonas noxia	strain=ATCC 43541	GCA_000160555.1	135083	135083	type	True	81.2662	432	797	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	80.5608	394	797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:22,877] [INFO] DFAST Taxonomy check result was written to GCF_030644225.1_ASM3064422v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:22,878] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:22,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:22,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/checkm_data
[2024-01-25 20:26:22,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:22,904] [INFO] Task started: CheckM
[2024-01-25 20:26:22,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030644225.1_ASM3064422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030644225.1_ASM3064422v1_genomic.fna/checkm_input GCF_030644225.1_ASM3064422v1_genomic.fna/checkm_result
[2024-01-25 20:26:47,230] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:47,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:47,248] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:47,248] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:47,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030644225.1_ASM3064422v1_genomic.fna/markers.fasta)
[2024-01-25 20:26:47,248] [INFO] Task started: Blastn
[2024-01-25 20:26:47,248] [INFO] Running command: blastn -query GCF_030644225.1_ASM3064422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e98e852-625e-4d48-bd5b-0ff4e66b62de/dqc_reference/reference_markers_gtdb.fasta -out GCF_030644225.1_ASM3064422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:48,096] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:48,099] [INFO] Selected 8 target genomes.
[2024-01-25 20:26:48,099] [INFO] Target genome list was writen to GCF_030644225.1_ASM3064422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:48,124] [INFO] Task started: fastANI
[2024-01-25 20:26:48,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgd854ccba-ccaa-4cee-abd4-587e85ef6fbf/GCF_030644225.1_ASM3064422v1_genomic.fna.gz --refList GCF_030644225.1_ASM3064422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030644225.1_ASM3064422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:26:53,839] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:53,846] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:26:53,846] [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_000234095.1	s__Centipeda infelix	86.9641	601	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372865.1	s__Centipeda sp905372865	85.5024	522	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717585.1	s__Centipeda sp001717585	85.165	556	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290285.1	s__Centipeda massiliensis	84.8094	554	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	97.87	97.87	0.91	0.91	2	-
GCF_001683335.1	s__Centipeda sp001683335	84.7453	612	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250475.1	s__Centipeda sp000318175	84.5591	555	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	96.58	96.58	0.89	0.89	2	-
GCF_000286455.1	s__Centipeda sp000286455	84.4513	497	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213975.1	s__Centipeda periodontii	84.3721	579	797	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	98.08	98.08	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:26:53,847] [INFO] GTDB search result was written to GCF_030644225.1_ASM3064422v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:26:53,848] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:26:53,850] [INFO] DFAST_QC result json was written to GCF_030644225.1_ASM3064422v1_genomic.fna/dqc_result.json
[2024-01-25 20:26:53,851] [INFO] DFAST_QC completed!
[2024-01-25 20:26:53,851] [INFO] Total running time: 0h0m48s