[2024-01-24 14:22:01,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference
[2024-01-24 14:22:02,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,680] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg48974d0a-3c67-4aa7-b68a-aaf9f736239f/GCF_003024675.1_ASM302467v1_genomic.fna.gz | prodigal -d GCF_003024675.1_ASM302467v1_genomic.fna/cds.fna -a GCF_003024675.1_ASM302467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:06,950] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:06,950] [INFO] Task started: HMMsearch
[2024-01-24 14:22:06,950] [INFO] Running command: hmmsearch --tblout GCF_003024675.1_ASM302467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/reference_markers.hmm GCF_003024675.1_ASM302467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:07,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:07,172] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48974d0a-3c67-4aa7-b68a-aaf9f736239f/GCF_003024675.1_ASM302467v1_genomic.fna.gz]
[2024-01-24 14:22:07,194] [INFO] Query marker FASTA was written to GCF_003024675.1_ASM302467v1_genomic.fna/markers.fasta
[2024-01-24 14:22:07,194] [INFO] Task started: Blastn
[2024-01-24 14:22:07,195] [INFO] Running command: blastn -query GCF_003024675.1_ASM302467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/reference_markers.fasta -out GCF_003024675.1_ASM302467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:07,766] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:07,770] [INFO] Selected 20 target genomes.
[2024-01-24 14:22:07,771] [INFO] Target genome list was writen to GCF_003024675.1_ASM302467v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:07,790] [INFO] Task started: fastANI
[2024-01-24 14:22:07,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg48974d0a-3c67-4aa7-b68a-aaf9f736239f/GCF_003024675.1_ASM302467v1_genomic.fna.gz --refList GCF_003024675.1_ASM302467v1_genomic.fna/target_genomes.txt --output GCF_003024675.1_ASM302467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:17,226] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:17,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:17,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:17,237] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:17,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:17,237] [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 faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	100.0	812	813	95	conclusive
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	89.7286	608	813	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.7897	213	813	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.6667	154	813	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	78.6577	217	813	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	78.4773	229	813	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	78.4442	223	813	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	78.3083	214	813	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	78.2311	226	813	95	below_threshold
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	78.0845	168	813	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.9319	178	813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:17,242] [INFO] DFAST Taxonomy check result was written to GCF_003024675.1_ASM302467v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:17,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:17,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:17,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/checkm_data
[2024-01-24 14:22:17,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:17,272] [INFO] Task started: CheckM
[2024-01-24 14:22:17,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024675.1_ASM302467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024675.1_ASM302467v1_genomic.fna/checkm_input GCF_003024675.1_ASM302467v1_genomic.fna/checkm_result
[2024-01-24 14:22:38,707] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:38,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:38,730] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:38,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:38,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024675.1_ASM302467v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:38,732] [INFO] Task started: Blastn
[2024-01-24 14:22:38,732] [INFO] Running command: blastn -query GCF_003024675.1_ASM302467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882993b4-052d-45bf-a465-c00eb4897a78/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024675.1_ASM302467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:39,645] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:39,649] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:39,649] [INFO] Target genome list was writen to GCF_003024675.1_ASM302467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:39,658] [INFO] Task started: fastANI
[2024-01-24 14:22:39,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg48974d0a-3c67-4aa7-b68a-aaf9f736239f/GCF_003024675.1_ASM302467v1_genomic.fna.gz --refList GCF_003024675.1_ASM302467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024675.1_ASM302467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:45,297] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:45,310] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:45,310] [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_003024675.1	s__Faecalibacillus faecis	100.0	812	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	conclusive
GCF_003024685.1	s__Faecalibacillus intestinalis	89.7286	608	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCA_900544435.1	s__Faecalibacillus sp900544435	88.6475	425	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	-
GCF_003480255.1	s__Faecalibacillus sp003480255	80.7777	340	813	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	78.9583	232	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	78.7014	217	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCA_910588075.1	s__MGBC163490 sp910588075	78.1102	186	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244545.1	s__Stoquefichus sp001244545	77.9108	213	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	98.22	98.22	0.87	0.87	2	-
GCA_018365815.1	s__Beduini sp018365815	77.5737	131	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Beduini	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:45,312] [INFO] GTDB search result was written to GCF_003024675.1_ASM302467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:45,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:45,316] [INFO] DFAST_QC result json was written to GCF_003024675.1_ASM302467v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:45,317] [INFO] DFAST_QC completed!
[2024-01-24 14:22:45,317] [INFO] Total running time: 0h0m44s