[2024-01-24 14:46:35,137] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference
[2024-01-24 14:46:36,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,335] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7328c4c-1dcb-4db7-8900-46d2b40c573e/GCF_009295725.1_ASM929572v1_genomic.fna.gz | prodigal -d GCF_009295725.1_ASM929572v1_genomic.fna/cds.fna -a GCF_009295725.1_ASM929572v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:41,440] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:41,441] [INFO] Task started: HMMsearch
[2024-01-24 14:46:41,441] [INFO] Running command: hmmsearch --tblout GCF_009295725.1_ASM929572v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/reference_markers.hmm GCF_009295725.1_ASM929572v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:41,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:41,770] [INFO] Found 6/6 markers.
[2024-01-24 14:46:41,811] [INFO] Query marker FASTA was written to GCF_009295725.1_ASM929572v1_genomic.fna/markers.fasta
[2024-01-24 14:46:41,811] [INFO] Task started: Blastn
[2024-01-24 14:46:41,812] [INFO] Running command: blastn -query GCF_009295725.1_ASM929572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/reference_markers.fasta -out GCF_009295725.1_ASM929572v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:42,498] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:42,505] [INFO] Selected 17 target genomes.
[2024-01-24 14:46:42,506] [INFO] Target genome list was writen to GCF_009295725.1_ASM929572v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:42,512] [INFO] Task started: fastANI
[2024-01-24 14:46:42,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7328c4c-1dcb-4db7-8900-46d2b40c573e/GCF_009295725.1_ASM929572v1_genomic.fna.gz --refList GCF_009295725.1_ASM929572v1_genomic.fna/target_genomes.txt --output GCF_009295725.1_ASM929572v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:53,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:53,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:53,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:53,899] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:46:53,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:46:53,900] [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
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	100.0	1006	1020	95	conclusive
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	78.598	351	1020	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	78.5508	342	1020	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	78.0807	265	1020	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	77.7242	239	1020	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.5333	292	1020	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.4643	243	1020	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	77.2803	269	1020	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.1748	172	1020	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.0461	228	1020	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.7225	169	1020	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.7211	271	1020	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.6738	198	1020	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.6619	221	1020	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.898	176	1020	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	75.7644	104	1020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:53,902] [INFO] DFAST Taxonomy check result was written to GCF_009295725.1_ASM929572v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:53,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:53,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:53,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/checkm_data
[2024-01-24 14:46:53,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:53,947] [INFO] Task started: CheckM
[2024-01-24 14:46:53,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009295725.1_ASM929572v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009295725.1_ASM929572v1_genomic.fna/checkm_input GCF_009295725.1_ASM929572v1_genomic.fna/checkm_result
[2024-01-24 14:47:16,615] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:16,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:16,641] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:16,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:16,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009295725.1_ASM929572v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:16,642] [INFO] Task started: Blastn
[2024-01-24 14:47:16,642] [INFO] Running command: blastn -query GCF_009295725.1_ASM929572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92742d94-188f-463e-b0d4-0fdccc5098eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009295725.1_ASM929572v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:17,475] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:17,481] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:17,481] [INFO] Target genome list was writen to GCF_009295725.1_ASM929572v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:17,496] [INFO] Task started: fastANI
[2024-01-24 14:47:17,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7328c4c-1dcb-4db7-8900-46d2b40c573e/GCF_009295725.1_ASM929572v1_genomic.fna.gz --refList GCF_009295725.1_ASM929572v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009295725.1_ASM929572v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:26,221] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:26,242] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:26,243] [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_009295725.1	s__Clostridium_P tarantellae	100.0	1006	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013285.1	s__Clostridium_P perfringens	78.5672	344	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_900456775.1	s__Clostridium_P ventriculi	78.0791	265	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_900091705.1	s__Clostridium_P mediterraneense	77.7112	240	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001403635.1	s__Clostridium_P massiliamazoniense	77.531	294	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129365.1	s__Clostridium_AH fallax	77.4678	264	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002327185.1	s__Clostridium chauvoei	77.421	246	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_003606265.1	s__Clostridium septicum	77.3723	276	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_900141845.1	s__Clostridium_AG cavendishii	77.2705	270	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	77.2009	174	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873245.1	s__Clostridium tertium	77.0368	229	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_001458595.1	s__Clostridium neonatale	76.6046	224	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_008152325.1	s__SY095 sp008152325	75.5971	74	1020	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__SY095	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:26,245] [INFO] GTDB search result was written to GCF_009295725.1_ASM929572v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:26,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:26,250] [INFO] DFAST_QC result json was written to GCF_009295725.1_ASM929572v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:26,251] [INFO] DFAST_QC completed!
[2024-01-24 14:47:26,251] [INFO] Total running time: 0h0m51s