[2023-06-18 23:17:57,556] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:57,558] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:57,558] [INFO] DQC Reference Directory: /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference
[2023-06-18 23:17:58,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:58,823] [INFO] Task started: Prodigal
[2023-06-18 23:17:58,824] [INFO] Running command: gunzip -c /var/lib/cwl/stga05ee496-c7c9-41bd-9a39-106e1f1c5129/GCA_018382255.1_ASM1838225v1_genomic.fna.gz | prodigal -d GCA_018382255.1_ASM1838225v1_genomic.fna/cds.fna -a GCA_018382255.1_ASM1838225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:18:02,432] [INFO] Task succeeded: Prodigal
[2023-06-18 23:18:02,432] [INFO] Task started: HMMsearch
[2023-06-18 23:18:02,432] [INFO] Running command: hmmsearch --tblout GCA_018382255.1_ASM1838225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/reference_markers.hmm GCA_018382255.1_ASM1838225v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:18:02,626] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:18:02,627] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga05ee496-c7c9-41bd-9a39-106e1f1c5129/GCA_018382255.1_ASM1838225v1_genomic.fna.gz]
[2023-06-18 23:18:02,656] [INFO] Query marker FASTA was written to GCA_018382255.1_ASM1838225v1_genomic.fna/markers.fasta
[2023-06-18 23:18:02,657] [INFO] Task started: Blastn
[2023-06-18 23:18:02,657] [INFO] Running command: blastn -query GCA_018382255.1_ASM1838225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/reference_markers.fasta -out GCA_018382255.1_ASM1838225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:03,336] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:03,339] [INFO] Selected 17 target genomes.
[2023-06-18 23:18:03,339] [INFO] Target genome list was writen to GCA_018382255.1_ASM1838225v1_genomic.fna/target_genomes.txt
[2023-06-18 23:18:03,340] [INFO] Task started: fastANI
[2023-06-18 23:18:03,340] [INFO] Running command: fastANI --query /var/lib/cwl/stga05ee496-c7c9-41bd-9a39-106e1f1c5129/GCA_018382255.1_ASM1838225v1_genomic.fna.gz --refList GCA_018382255.1_ASM1838225v1_genomic.fna/target_genomes.txt --output GCA_018382255.1_ASM1838225v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:18:10,250] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:10,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:18:10,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:18:10,261] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:18:10,261] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:18:10,261] [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
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	92.3515	318	469	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	88.9328	298	469	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	78.7847	112	469	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.73	116	469	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	78.4528	122	469	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	78.4445	120	469	95	below_threshold
Erysipelatoclostridium ramosum	strain=FDAARGOS_906	GCA_016027135.1	1547	1547	type	True	78.4392	123	469	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	78.2022	108	469	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.9429	92	469	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.6631	102	469	95	below_threshold
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	76.7535	68	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:18:10,263] [INFO] DFAST Taxonomy check result was written to GCA_018382255.1_ASM1838225v1_genomic.fna/tc_result.tsv
[2023-06-18 23:18:10,264] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:18:10,264] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:18:10,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/checkm_data
[2023-06-18 23:18:10,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:18:10,292] [INFO] Task started: CheckM
[2023-06-18 23:18:10,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018382255.1_ASM1838225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018382255.1_ASM1838225v1_genomic.fna/checkm_input GCA_018382255.1_ASM1838225v1_genomic.fna/checkm_result
[2023-06-18 23:18:27,798] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:27,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:27,821] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:27,821] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:27,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018382255.1_ASM1838225v1_genomic.fna/markers.fasta)
[2023-06-18 23:18:27,822] [INFO] Task started: Blastn
[2023-06-18 23:18:27,822] [INFO] Running command: blastn -query GCA_018382255.1_ASM1838225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge30a3585-1943-4b17-8c7d-2aacfe997e10/dqc_reference/reference_markers_gtdb.fasta -out GCA_018382255.1_ASM1838225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:28,523] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:28,527] [INFO] Selected 10 target genomes.
[2023-06-18 23:18:28,528] [INFO] Target genome list was writen to GCA_018382255.1_ASM1838225v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:28,530] [INFO] Task started: fastANI
[2023-06-18 23:18:28,530] [INFO] Running command: fastANI --query /var/lib/cwl/stga05ee496-c7c9-41bd-9a39-106e1f1c5129/GCA_018382255.1_ASM1838225v1_genomic.fna.gz --refList GCA_018382255.1_ASM1838225v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018382255.1_ASM1838225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:32,722] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:32,730] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:18:32,731] [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_900544435.1	s__Faecalibacillus sp900544435	97.8267	305	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	conclusive
GCF_003024685.1	s__Faecalibacillus intestinalis	92.3515	318	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCF_003024675.1	s__Faecalibacillus faecis	88.9328	298	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	-
GCF_003480255.1	s__Faecalibacillus sp003480255	81.2567	192	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCF_016901755.1	s__Faecalibacillus spiroforme_A	79.0219	137	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
GCF_014131695.1	s__Erysipelatoclostridium ramosum	78.4833	121	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	-
GCF_002160815.1	s__Massiliomicrobiota merdigallinarum	78.2852	106	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	98.05	97.64	0.81	0.77	12	-
GCA_002359025.1	s__UBA3379 sp002359025	77.6548	77	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__UBA3379	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:32,732] [INFO] GTDB search result was written to GCA_018382255.1_ASM1838225v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:32,733] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:32,736] [INFO] DFAST_QC result json was written to GCA_018382255.1_ASM1838225v1_genomic.fna/dqc_result.json
[2023-06-18 23:18:32,736] [INFO] DFAST_QC completed!
[2023-06-18 23:18:32,736] [INFO] Total running time: 0h0m35s