[2024-01-24 13:57:55,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference
[2024-01-24 13:57:57,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,221] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,222] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9739dd5-0fcd-41c8-901c-79226d03539c/GCF_009695655.1_ASM969565v1_genomic.fna.gz | prodigal -d GCF_009695655.1_ASM969565v1_genomic.fna/cds.fna -a GCF_009695655.1_ASM969565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:02,728] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:02,728] [INFO] Task started: HMMsearch
[2024-01-24 13:58:02,729] [INFO] Running command: hmmsearch --tblout GCF_009695655.1_ASM969565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/reference_markers.hmm GCF_009695655.1_ASM969565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:03,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:03,029] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9739dd5-0fcd-41c8-901c-79226d03539c/GCF_009695655.1_ASM969565v1_genomic.fna.gz]
[2024-01-24 13:58:03,054] [INFO] Query marker FASTA was written to GCF_009695655.1_ASM969565v1_genomic.fna/markers.fasta
[2024-01-24 13:58:03,054] [INFO] Task started: Blastn
[2024-01-24 13:58:03,054] [INFO] Running command: blastn -query GCF_009695655.1_ASM969565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/reference_markers.fasta -out GCF_009695655.1_ASM969565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:03,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:03,685] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:03,686] [INFO] Target genome list was writen to GCF_009695655.1_ASM969565v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:03,694] [INFO] Task started: fastANI
[2024-01-24 13:58:03,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9739dd5-0fcd-41c8-901c-79226d03539c/GCF_009695655.1_ASM969565v1_genomic.fna.gz --refList GCF_009695655.1_ASM969565v1_genomic.fna/target_genomes.txt --output GCF_009695655.1_ASM969565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,459] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:11,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:11,460] [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
Sharpea porci	strain=CA-Schmier-601-WT-3	GCA_009695655.1	2652286	2652286	type	True	100.0	789	794	95	conclusive
Sharpea azabuensis	strain=DSM 18934	GCA_000702165.1	322505	322505	type	True	88.8995	591	794	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	78.1595	136	794	95	below_threshold
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	78.0448	143	794	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	78.0358	134	794	95	below_threshold
Intestinibaculum porci	strain=SG0102	GCA_003925875.1	2487118	2487118	type	True	77.856	132	794	95	below_threshold
Eggerthia catenaformis	strain=DSM 20559	GCA_000422605.1	31973	31973	type	True	77.6345	102	794	95	below_threshold
Eggerthia catenaformis	strain=OT 569	GCA_000340375.1	31973	31973	type	True	77.6076	105	794	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.3743	59	794	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.1371	87	794	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.0674	81	794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,462] [INFO] DFAST Taxonomy check result was written to GCF_009695655.1_ASM969565v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/checkm_data
[2024-01-24 13:58:11,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,492] [INFO] Task started: CheckM
[2024-01-24 13:58:11,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695655.1_ASM969565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695655.1_ASM969565v1_genomic.fna/checkm_input GCF_009695655.1_ASM969565v1_genomic.fna/checkm_result
[2024-01-24 13:58:35,597] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:35,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,629] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:35,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:35,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695655.1_ASM969565v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:35,630] [INFO] Task started: Blastn
[2024-01-24 13:58:35,631] [INFO] Running command: blastn -query GCF_009695655.1_ASM969565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3b6ed1-b7d1-4683-89cd-03f8a8c41265/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695655.1_ASM969565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:36,503] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:36,507] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:36,508] [INFO] Target genome list was writen to GCF_009695655.1_ASM969565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:36,518] [INFO] Task started: fastANI
[2024-01-24 13:58:36,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9739dd5-0fcd-41c8-901c-79226d03539c/GCF_009695655.1_ASM969565v1_genomic.fna.gz --refList GCF_009695655.1_ASM969565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695655.1_ASM969565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:41,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:41,150] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:41,151] [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_009695655.1	s__Sharpea porci	100.0	789	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Sharpea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000702165.1	s__Sharpea azabuensis	88.8972	592	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Sharpea	95.0	98.40	97.32	0.90	0.79	46	-
GCF_004168205.1	s__Catenibacterium sp000437715	78.2727	119	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900540665.1	s__Catenibacterium sp900540665	78.0141	112	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	-
GCA_900540685.1	s__Catenibacterium sp900540685	77.9045	120	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000173795.1	s__Catenibacterium mitsuokai	77.8765	132	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	-
GCA_900764725.1	s__Catenibacterium sp900764725	77.8507	112	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764565.1	s__Catenibacterium sp900764565	77.585	109	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340375.1	s__Eggerthia catenaformis	77.5784	106	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Eggerthia	95.0	98.71	98.60	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,153] [INFO] GTDB search result was written to GCF_009695655.1_ASM969565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:41,154] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:41,158] [INFO] DFAST_QC result json was written to GCF_009695655.1_ASM969565v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:41,159] [INFO] DFAST_QC completed!
[2024-01-24 13:58:41,159] [INFO] Total running time: 0h0m45s