[2024-01-24 13:01:25,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:25,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:25,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference
[2024-01-24 13:01:26,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,943] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg87e8ad84-cfa0-476e-86fb-dc8e4359d87e/GCF_001078375.1_ASM107837v1_genomic.fna.gz | prodigal -d GCF_001078375.1_ASM107837v1_genomic.fna/cds.fna -a GCF_001078375.1_ASM107837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:32,011] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:32,011] [INFO] Task started: HMMsearch
[2024-01-24 13:01:32,011] [INFO] Running command: hmmsearch --tblout GCF_001078375.1_ASM107837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/reference_markers.hmm GCF_001078375.1_ASM107837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:32,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:32,290] [INFO] Found 6/6 markers.
[2024-01-24 13:01:32,325] [INFO] Query marker FASTA was written to GCF_001078375.1_ASM107837v1_genomic.fna/markers.fasta
[2024-01-24 13:01:32,325] [INFO] Task started: Blastn
[2024-01-24 13:01:32,326] [INFO] Running command: blastn -query GCF_001078375.1_ASM107837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/reference_markers.fasta -out GCF_001078375.1_ASM107837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:32,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:32,947] [INFO] Selected 8 target genomes.
[2024-01-24 13:01:32,948] [INFO] Target genome list was writen to GCF_001078375.1_ASM107837v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:32,955] [INFO] Task started: fastANI
[2024-01-24 13:01:32,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e8ad84-cfa0-476e-86fb-dc8e4359d87e/GCF_001078375.1_ASM107837v1_genomic.fna.gz --refList GCF_001078375.1_ASM107837v1_genomic.fna/target_genomes.txt --output GCF_001078375.1_ASM107837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:36,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:36,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:36,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:36,895] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:36,895] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:36,896] [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
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	100.0	701	702	95	conclusive
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	88.9057	565	702	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	88.8822	561	702	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	88.8211	552	702	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	84.4768	468	702	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	84.037	448	702	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	80.9765	332	702	95	below_threshold
Veillonella criceti	strain=NCTC12020	GCA_900460315.1	103891	103891	type	True	78.1845	113	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:36,899] [INFO] DFAST Taxonomy check result was written to GCF_001078375.1_ASM107837v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:36,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:36,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:36,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/checkm_data
[2024-01-24 13:01:36,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:36,931] [INFO] Task started: CheckM
[2024-01-24 13:01:36,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001078375.1_ASM107837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001078375.1_ASM107837v1_genomic.fna/checkm_input GCF_001078375.1_ASM107837v1_genomic.fna/checkm_result
[2024-01-24 13:01:58,449] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:58,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:58,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:58,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:58,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001078375.1_ASM107837v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:58,471] [INFO] Task started: Blastn
[2024-01-24 13:01:58,471] [INFO] Running command: blastn -query GCF_001078375.1_ASM107837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg421a64f1-039c-47b8-bb76-df3d8e5359b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001078375.1_ASM107837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:59,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:59,277] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:59,277] [INFO] Target genome list was writen to GCF_001078375.1_ASM107837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:59,288] [INFO] Task started: fastANI
[2024-01-24 13:01:59,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e8ad84-cfa0-476e-86fb-dc8e4359d87e/GCF_001078375.1_ASM107837v1_genomic.fna.gz --refList GCF_001078375.1_ASM107837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001078375.1_ASM107837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:05,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:05,262] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:05,262] [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_001078375.1	s__Veillonella tobetsuensis	100.0	701	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	conclusive
GCF_002959915.1	s__Veillonella atypica	88.9057	565	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCA_905214495.1	s__Veillonella sp905214495	87.2071	432	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550175.1	s__Veillonella sp900550175	84.481	345	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.03	98.03	0.91	0.91	2	-
GCF_013393365.1	s__Veillonella nakazawae	84.4648	466	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	-
GCF_002959895.1	s__Veillonella infantium	84.0099	449	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCF_002959755.1	s__Veillonella sp002959755	83.6996	455	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556785.1	s__Veillonella sp900556785	83.1402	311	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018367495.1	s__Veillonella sp018367495	82.5574	370	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902834965.1	s__Veillonella sp902834965	82.2054	229	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757715.1	s__Veillonella sp900757715	81.6364	360	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.4547	97.81	97.81	0.74	0.74	2	-
GCF_003992125.1	s__Veillonella caviae	80.9567	333	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	-
GCF_900460315.1	s__Veillonella_A criceti	78.1395	110	702	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:05,263] [INFO] GTDB search result was written to GCF_001078375.1_ASM107837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:05,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:05,271] [INFO] DFAST_QC result json was written to GCF_001078375.1_ASM107837v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:05,271] [INFO] DFAST_QC completed!
[2024-01-24 13:02:05,272] [INFO] Total running time: 0h0m40s