[2024-01-24 12:53:51,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:51,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:51,698] [INFO] DQC Reference Directory: /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference
[2024-01-24 12:53:52,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:52,887] [INFO] Task started: Prodigal
[2024-01-24 12:53:52,887] [INFO] Running command: gunzip -c /var/lib/cwl/stga6067511-2114-4645-a77d-1ac201876104/GCF_025148785.1_ASM2514878v1_genomic.fna.gz | prodigal -d GCF_025148785.1_ASM2514878v1_genomic.fna/cds.fna -a GCF_025148785.1_ASM2514878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:57,853] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:57,854] [INFO] Task started: HMMsearch
[2024-01-24 12:53:57,854] [INFO] Running command: hmmsearch --tblout GCF_025148785.1_ASM2514878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/reference_markers.hmm GCF_025148785.1_ASM2514878v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:58,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:58,116] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga6067511-2114-4645-a77d-1ac201876104/GCF_025148785.1_ASM2514878v1_genomic.fna.gz]
[2024-01-24 12:53:58,144] [INFO] Query marker FASTA was written to GCF_025148785.1_ASM2514878v1_genomic.fna/markers.fasta
[2024-01-24 12:53:58,144] [INFO] Task started: Blastn
[2024-01-24 12:53:58,144] [INFO] Running command: blastn -query GCF_025148785.1_ASM2514878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/reference_markers.fasta -out GCF_025148785.1_ASM2514878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:58,771] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:58,775] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:58,775] [INFO] Target genome list was writen to GCF_025148785.1_ASM2514878v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:58,847] [INFO] Task started: fastANI
[2024-01-24 12:53:58,847] [INFO] Running command: fastANI --query /var/lib/cwl/stga6067511-2114-4645-a77d-1ac201876104/GCF_025148785.1_ASM2514878v1_genomic.fna.gz --refList GCF_025148785.1_ASM2514878v1_genomic.fna/target_genomes.txt --output GCF_025148785.1_ASM2514878v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:06,203] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:06,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:06,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:06,215] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:06,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:06,216] [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
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	100.0	880	883	95	conclusive
Intestinibaculum porci	strain=SG0102	GCA_003925875.1	2487118	2487118	type	True	78.9108	120	883	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	78.2871	153	883	95	below_threshold
Sharpea azabuensis	strain=DSM 18934	GCA_000702165.1	322505	322505	type	True	78.2116	139	883	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	78.2018	102	883	95	below_threshold
Eggerthia catenaformis	strain=OT 569	GCA_000340375.1	31973	31973	type	True	78.1522	107	883	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	78.037	149	883	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	77.4197	69	883	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.2336	124	883	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	77.027	66	883	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	76.9929	126	883	95	below_threshold
Eggerthia catenaformis	strain=DSM 20559	GCA_000422605.1	31973	31973	type	True	76.9396	99	883	95	below_threshold
[Clostridium] cocleatum	strain=ATCC 29902	GCA_002803405.1	69824	69824	type	True	76.8179	68	883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:06,217] [INFO] DFAST Taxonomy check result was written to GCF_025148785.1_ASM2514878v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:06,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:06,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:06,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/checkm_data
[2024-01-24 12:54:06,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:06,247] [INFO] Task started: CheckM
[2024-01-24 12:54:06,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025148785.1_ASM2514878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025148785.1_ASM2514878v1_genomic.fna/checkm_input GCF_025148785.1_ASM2514878v1_genomic.fna/checkm_result
[2024-01-24 12:54:28,178] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:28,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:28,204] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:28,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:28,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025148785.1_ASM2514878v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:28,205] [INFO] Task started: Blastn
[2024-01-24 12:54:28,205] [INFO] Running command: blastn -query GCF_025148785.1_ASM2514878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2cf019d-a80f-423e-a437-50039e55f472/dqc_reference/reference_markers_gtdb.fasta -out GCF_025148785.1_ASM2514878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:29,052] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:29,055] [INFO] Selected 6 target genomes.
[2024-01-24 12:54:29,056] [INFO] Target genome list was writen to GCF_025148785.1_ASM2514878v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:29,060] [INFO] Task started: fastANI
[2024-01-24 12:54:29,061] [INFO] Running command: fastANI --query /var/lib/cwl/stga6067511-2114-4645-a77d-1ac201876104/GCF_025148785.1_ASM2514878v1_genomic.fna.gz --refList GCF_025148785.1_ASM2514878v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025148785.1_ASM2514878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:33,138] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:33,145] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:33,146] [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_000173795.1	s__Catenibacterium mitsuokai	99.8247	738	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	conclusive
GCA_900540665.1	s__Catenibacterium sp900540665	94.1003	578	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	-
GCF_004168205.1	s__Catenibacterium sp000437715	93.6777	577	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900764565.1	s__Catenibacterium sp900764565	93.2133	502	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540685.1	s__Catenibacterium sp900540685	92.635	580	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCA_900764725.1	s__Catenibacterium sp900764725	91.3958	523	883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:33,147] [INFO] GTDB search result was written to GCF_025148785.1_ASM2514878v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:33,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:33,151] [INFO] DFAST_QC result json was written to GCF_025148785.1_ASM2514878v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:33,152] [INFO] DFAST_QC completed!
[2024-01-24 12:54:33,152] [INFO] Total running time: 0h0m41s