[2024-01-25 20:17:35,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:35,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:35,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference
[2024-01-25 20:17:36,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:36,882] [INFO] Task started: Prodigal
[2024-01-25 20:17:36,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0baab11-e9b6-442e-afda-6b591ed1dea6/GCF_900637075.1_48128_D02_genomic.fna.gz | prodigal -d GCF_900637075.1_48128_D02_genomic.fna/cds.fna -a GCF_900637075.1_48128_D02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:40,588] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:40,589] [INFO] Task started: HMMsearch
[2024-01-25 20:17:40,589] [INFO] Running command: hmmsearch --tblout GCF_900637075.1_48128_D02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/reference_markers.hmm GCF_900637075.1_48128_D02_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:40,790] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:40,791] [INFO] Found 6/6 markers.
[2024-01-25 20:17:40,818] [INFO] Query marker FASTA was written to GCF_900637075.1_48128_D02_genomic.fna/markers.fasta
[2024-01-25 20:17:40,819] [INFO] Task started: Blastn
[2024-01-25 20:17:40,819] [INFO] Running command: blastn -query GCF_900637075.1_48128_D02_genomic.fna/markers.fasta -db /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/reference_markers.fasta -out GCF_900637075.1_48128_D02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:41,358] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:41,361] [INFO] Selected 15 target genomes.
[2024-01-25 20:17:41,361] [INFO] Target genome list was writen to GCF_900637075.1_48128_D02_genomic.fna/target_genomes.txt
[2024-01-25 20:17:41,367] [INFO] Task started: fastANI
[2024-01-25 20:17:41,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0baab11-e9b6-442e-afda-6b591ed1dea6/GCF_900637075.1_48128_D02_genomic.fna.gz --refList GCF_900637075.1_48128_D02_genomic.fna/target_genomes.txt --output GCF_900637075.1_48128_D02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:47,345] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:47,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:47,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:47,353] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:17:47,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:47,353] [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 pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	100.0	714	718	95	conclusive
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	99.9963	704	718	95	conclusive
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	88.9225	582	718	95	below_threshold
Streptococcus bovimastitidis	strain=NZ1587	GCA_001885095.1	1856638	1856638	type	True	80.313	336	718	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	80.0717	72	718	95	below_threshold
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	80.0685	330	718	95	below_threshold
Streptococcus uberis	strain=NCTC3858	GCA_900475595.1	1349	1349	type	True	80.0436	242	718	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	79.2892	194	718	95	below_threshold
Streptococcus parauberis	strain=NCFD 2020	GCA_000187935.2	1348	1348	type	True	79.1787	223	718	95	below_threshold
Streptococcus equi	strain=ATCC 33398	GCA_900156215.1	1336	1336	type	True	78.8563	131	718	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	78.2711	100	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:47,356] [INFO] DFAST Taxonomy check result was written to GCF_900637075.1_48128_D02_genomic.fna/tc_result.tsv
[2024-01-25 20:17:47,356] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:47,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:47,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/checkm_data
[2024-01-25 20:17:47,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:47,381] [INFO] Task started: CheckM
[2024-01-25 20:17:47,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637075.1_48128_D02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637075.1_48128_D02_genomic.fna/checkm_input GCF_900637075.1_48128_D02_genomic.fna/checkm_result
[2024-01-25 20:18:05,178] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:05,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:05,201] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:05,201] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:05,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637075.1_48128_D02_genomic.fna/markers.fasta)
[2024-01-25 20:18:05,202] [INFO] Task started: Blastn
[2024-01-25 20:18:05,202] [INFO] Running command: blastn -query GCF_900637075.1_48128_D02_genomic.fna/markers.fasta -db /var/lib/cwl/stg634ffd88-8bb1-4e2d-84e9-704a275c5e61/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637075.1_48128_D02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:05,998] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:06,005] [INFO] Selected 11 target genomes.
[2024-01-25 20:18:06,005] [INFO] Target genome list was writen to GCF_900637075.1_48128_D02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:06,017] [INFO] Task started: fastANI
[2024-01-25 20:18:06,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0baab11-e9b6-442e-afda-6b591ed1dea6/GCF_900637075.1_48128_D02_genomic.fna.gz --refList GCF_900637075.1_48128_D02_genomic.fna/target_genomes_gtdb.txt --output GCF_900637075.1_48128_D02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:10,977] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:10,984] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:10,985] [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_000188035.1	s__Streptococcus pseudoporcinus	99.9961	705	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	conclusive
GCF_900475415.1	s__Streptococcus porcinus	88.9401	583	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_901542335.1	s__Streptococcus porcinus_A	88.7232	581	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_001885095.1	s__Streptococcus bovimastitidis	80.3132	336	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475595.1	s__Streptococcus uberis	80.1193	243	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.97	98.11	0.91	0.87	68	-
GCF_002887775.1	s__Streptococcus penaeicida	80.0686	330	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188015.2	s__Streptococcus ictaluri	79.5381	169	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380005.1	s__Streptococcus didelphis	79.2892	194	718	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	79.2294	223	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_003674745.1	s__Streptococcus iniae	79.0424	214	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_003686955.1	s__Streptococcus sp003686955	78.2711	100	718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:10,986] [INFO] GTDB search result was written to GCF_900637075.1_48128_D02_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:10,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:10,989] [INFO] DFAST_QC result json was written to GCF_900637075.1_48128_D02_genomic.fna/dqc_result.json
[2024-01-25 20:18:10,989] [INFO] DFAST_QC completed!
[2024-01-25 20:18:10,989] [INFO] Total running time: 0h0m35s