[2024-01-24 15:26:39,866] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,867] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference
[2024-01-24 15:26:41,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,232] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg3490f668-db94-4c7a-a636-934532ac230a/GCF_002887775.1_ASM288777v1_genomic.fna.gz | prodigal -d GCF_002887775.1_ASM288777v1_genomic.fna/cds.fna -a GCF_002887775.1_ASM288777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:45,461] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:45,461] [INFO] Task started: HMMsearch
[2024-01-24 15:26:45,461] [INFO] Running command: hmmsearch --tblout GCF_002887775.1_ASM288777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/reference_markers.hmm GCF_002887775.1_ASM288777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:45,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:45,726] [INFO] Found 6/6 markers.
[2024-01-24 15:26:45,749] [INFO] Query marker FASTA was written to GCF_002887775.1_ASM288777v1_genomic.fna/markers.fasta
[2024-01-24 15:26:45,749] [INFO] Task started: Blastn
[2024-01-24 15:26:45,749] [INFO] Running command: blastn -query GCF_002887775.1_ASM288777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/reference_markers.fasta -out GCF_002887775.1_ASM288777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:46,833] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:46,837] [INFO] Selected 13 target genomes.
[2024-01-24 15:26:46,837] [INFO] Target genome list was writen to GCF_002887775.1_ASM288777v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:47,258] [INFO] Task started: fastANI
[2024-01-24 15:26:47,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg3490f668-db94-4c7a-a636-934532ac230a/GCF_002887775.1_ASM288777v1_genomic.fna.gz --refList GCF_002887775.1_ASM288777v1_genomic.fna/target_genomes.txt --output GCF_002887775.1_ASM288777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:52,357] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:52,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:52,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:52,368] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:52,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:52,368] [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
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	100.0	656	657	95	conclusive
Streptococcus bovimastitidis	strain=NZ1587	GCA_001885095.1	1856638	1856638	type	True	93.2227	555	657	95	below_threshold
Streptococcus parauberis	strain=NCFD 2020	GCA_000187935.2	1348	1348	type	True	81.0703	272	657	95	below_threshold
Streptococcus uberis	strain=NCTC3858	GCA_900475595.1	1349	1349	type	True	80.3081	326	657	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	80.2255	328	657	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	79.9631	322	657	95	below_threshold
Streptococcus pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	79.9501	327	657	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	79.2086	172	657	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.5133	81	657	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.0407	85	657	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.9693	59	657	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	77.8039	81	657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:52,370] [INFO] DFAST Taxonomy check result was written to GCF_002887775.1_ASM288777v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:52,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:52,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:52,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/checkm_data
[2024-01-24 15:26:52,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:52,395] [INFO] Task started: CheckM
[2024-01-24 15:26:52,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002887775.1_ASM288777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002887775.1_ASM288777v1_genomic.fna/checkm_input GCF_002887775.1_ASM288777v1_genomic.fna/checkm_result
[2024-01-24 15:27:15,123] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:15,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:15,168] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:15,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:15,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002887775.1_ASM288777v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:15,172] [INFO] Task started: Blastn
[2024-01-24 15:27:15,172] [INFO] Running command: blastn -query GCF_002887775.1_ASM288777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469501bb-2b85-4f26-a324-8375be89a3a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002887775.1_ASM288777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:16,314] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:16,318] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:16,318] [INFO] Target genome list was writen to GCF_002887775.1_ASM288777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:16,325] [INFO] Task started: fastANI
[2024-01-24 15:27:16,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg3490f668-db94-4c7a-a636-934532ac230a/GCF_002887775.1_ASM288777v1_genomic.fna.gz --refList GCF_002887775.1_ASM288777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002887775.1_ASM288777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:20,739] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:20,751] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:20,751] [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_002887775.1	s__Streptococcus penaeicida	100.0	656	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001885095.1	s__Streptococcus bovimastitidis	93.2227	555	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187935.1	s__Streptococcus parauberis	81.0703	272	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_900475595.1	s__Streptococcus uberis	80.3191	325	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.97	98.11	0.91	0.87	68	-
GCF_901542335.1	s__Streptococcus porcinus_A	80.3048	324	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_900475415.1	s__Streptococcus porcinus	80.2255	328	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	79.9634	322	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_000188015.2	s__Streptococcus ictaluri	79.3964	175	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785785.1	s__Streptococcus uberis_A	79.2994	249	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:20,753] [INFO] GTDB search result was written to GCF_002887775.1_ASM288777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:20,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:20,758] [INFO] DFAST_QC result json was written to GCF_002887775.1_ASM288777v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:20,759] [INFO] DFAST_QC completed!
[2024-01-24 15:27:20,759] [INFO] Total running time: 0h0m41s