[2024-01-24 12:14:49,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,055] [INFO] DQC Reference Directory: /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference
[2024-01-24 12:14:50,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,341] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,342] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd70155c-6dd7-4c3a-af7d-ea2afd8d1a97/GCF_024399475.1_ASM2439947v1_genomic.fna.gz | prodigal -d GCF_024399475.1_ASM2439947v1_genomic.fna/cds.fna -a GCF_024399475.1_ASM2439947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:56,557] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:56,557] [INFO] Task started: HMMsearch
[2024-01-24 12:14:56,557] [INFO] Running command: hmmsearch --tblout GCF_024399475.1_ASM2439947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/reference_markers.hmm GCF_024399475.1_ASM2439947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:56,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:56,822] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd70155c-6dd7-4c3a-af7d-ea2afd8d1a97/GCF_024399475.1_ASM2439947v1_genomic.fna.gz]
[2024-01-24 12:14:56,855] [INFO] Query marker FASTA was written to GCF_024399475.1_ASM2439947v1_genomic.fna/markers.fasta
[2024-01-24 12:14:56,855] [INFO] Task started: Blastn
[2024-01-24 12:14:56,855] [INFO] Running command: blastn -query GCF_024399475.1_ASM2439947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/reference_markers.fasta -out GCF_024399475.1_ASM2439947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:57,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:57,535] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:57,536] [INFO] Target genome list was writen to GCF_024399475.1_ASM2439947v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:57,542] [INFO] Task started: fastANI
[2024-01-24 12:14:57,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd70155c-6dd7-4c3a-af7d-ea2afd8d1a97/GCF_024399475.1_ASM2439947v1_genomic.fna.gz --refList GCF_024399475.1_ASM2439947v1_genomic.fna/target_genomes.txt --output GCF_024399475.1_ASM2439947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:05,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:05,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:05,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:05,076] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:05,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:05,077] [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
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	80.5757	425	977	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	80.5114	426	977	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	79.6832	391	977	95	below_threshold
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	79.3984	374	977	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	78.3828	196	977	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.3302	176	977	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.2482	131	977	95	below_threshold
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	78.064	108	977	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	77.5783	167	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,078] [INFO] DFAST Taxonomy check result was written to GCF_024399475.1_ASM2439947v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:05,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:05,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:05,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/checkm_data
[2024-01-24 12:15:05,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:05,112] [INFO] Task started: CheckM
[2024-01-24 12:15:05,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024399475.1_ASM2439947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024399475.1_ASM2439947v1_genomic.fna/checkm_input GCF_024399475.1_ASM2439947v1_genomic.fna/checkm_result
[2024-01-24 12:15:30,081] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:30,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:30,102] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:30,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:30,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024399475.1_ASM2439947v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:30,103] [INFO] Task started: Blastn
[2024-01-24 12:15:30,104] [INFO] Running command: blastn -query GCF_024399475.1_ASM2439947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17ed0f5-7719-4865-acae-efcd7f837eaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_024399475.1_ASM2439947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:30,971] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:30,976] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:30,977] [INFO] Target genome list was writen to GCF_024399475.1_ASM2439947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:30,995] [INFO] Task started: fastANI
[2024-01-24 12:15:30,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd70155c-6dd7-4c3a-af7d-ea2afd8d1a97/GCF_024399475.1_ASM2439947v1_genomic.fna.gz --refList GCF_024399475.1_ASM2439947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024399475.1_ASM2439947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:38,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:38,665] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:38,665] [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_002160865.1	s__Massiliomicrobiota sp002160865	84.6665	588	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	97.99	97.96	0.87	0.83	4	-
GCF_002160815.1	s__Massiliomicrobiota merdigallinarum	83.9867	551	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	98.05	97.64	0.81	0.77	12	-
GCA_900538465.1	s__Longibaculum sp900538465	80.5612	401	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343035.1	s__Longibaculum muris	80.4722	429	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	98.90	96.51	0.88	0.82	7	-
GCF_001244545.1	s__Stoquefichus sp001244545	80.0859	424	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	98.22	98.22	0.87	0.87	2	-
GCF_000455285.1	s__Stoquefichus massiliensis	79.9982	401	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_910588075.1	s__MGBC163490 sp910588075	79.7401	319	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009767585.1	s__Coprobacillus cateniformis	79.6532	390	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus	95.0	99.28	99.05	0.92	0.87	12	-
GCA_002359025.1	s__UBA3379 sp002359025	79.3961	245	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__UBA3379	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586805.1	s__MGBC140090 sp910586805	79.0458	268	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC140090	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579135.1	s__MGBC113645 sp910579135	78.6464	252	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC113645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003480255.1	s__Faecalibacillus sp003480255	78.2846	192	977	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:38,667] [INFO] GTDB search result was written to GCF_024399475.1_ASM2439947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:38,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:38,671] [INFO] DFAST_QC result json was written to GCF_024399475.1_ASM2439947v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:38,671] [INFO] DFAST_QC completed!
[2024-01-24 12:15:38,671] [INFO] Total running time: 0h0m50s