[2024-01-24 13:49:12,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:12,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:12,758] [INFO] DQC Reference Directory: /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference
[2024-01-24 13:49:14,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,004] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,004] [INFO] Running command: gunzip -c /var/lib/cwl/stgc61ae629-6f4a-4e8d-b28e-50d057000443/GCF_900459215.1_44087_A02_genomic.fna.gz | prodigal -d GCF_900459215.1_44087_A02_genomic.fna/cds.fna -a GCF_900459215.1_44087_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:19,559] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:19,560] [INFO] Task started: HMMsearch
[2024-01-24 13:49:19,560] [INFO] Running command: hmmsearch --tblout GCF_900459215.1_44087_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/reference_markers.hmm GCF_900459215.1_44087_A02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:19,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:19,798] [INFO] Found 6/6 markers.
[2024-01-24 13:49:19,822] [INFO] Query marker FASTA was written to GCF_900459215.1_44087_A02_genomic.fna/markers.fasta
[2024-01-24 13:49:19,823] [INFO] Task started: Blastn
[2024-01-24 13:49:19,823] [INFO] Running command: blastn -query GCF_900459215.1_44087_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/reference_markers.fasta -out GCF_900459215.1_44087_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:20,404] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:20,407] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:20,407] [INFO] Target genome list was writen to GCF_900459215.1_44087_A02_genomic.fna/target_genomes.txt
[2024-01-24 13:49:20,419] [INFO] Task started: fastANI
[2024-01-24 13:49:20,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61ae629-6f4a-4e8d-b28e-50d057000443/GCF_900459215.1_44087_A02_genomic.fna.gz --refList GCF_900459215.1_44087_A02_genomic.fna/target_genomes.txt --output GCF_900459215.1_44087_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,238] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:27,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:27,238] [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 criceti	strain=NCTC12277	GCA_900459215.1	1333	1333	type	True	100.0	804	806	95	conclusive
Streptococcus criceti	strain=HS-6	GCA_000187975.3	1333	1333	type	True	99.9965	797	806	95	conclusive
Streptococcus sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	80.517	403	806	95	below_threshold
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	80.3791	388	806	95	below_threshold
Streptococcus sobrinus	strain=ATCC 33478	GCA_000439045.1	1310	1310	type	True	80.2165	399	806	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	78.1267	92	806	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	77.8894	78	806	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	77.8494	114	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,367] [INFO] DFAST Taxonomy check result was written to GCF_900459215.1_44087_A02_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/checkm_data
[2024-01-24 13:49:27,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,405] [INFO] Task started: CheckM
[2024-01-24 13:49:27,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459215.1_44087_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459215.1_44087_A02_genomic.fna/checkm_input GCF_900459215.1_44087_A02_genomic.fna/checkm_result
[2024-01-24 13:49:50,596] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:50,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,616] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:50,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:50,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459215.1_44087_A02_genomic.fna/markers.fasta)
[2024-01-24 13:49:50,616] [INFO] Task started: Blastn
[2024-01-24 13:49:50,617] [INFO] Running command: blastn -query GCF_900459215.1_44087_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36c3894-c2f0-45d0-856c-17379b825a05/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459215.1_44087_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,437] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:51,438] [INFO] Target genome list was writen to GCF_900459215.1_44087_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,445] [INFO] Task started: fastANI
[2024-01-24 13:49:51,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61ae629-6f4a-4e8d-b28e-50d057000443/GCF_900459215.1_44087_A02_genomic.fna.gz --refList GCF_900459215.1_44087_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900459215.1_44087_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:57,553] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,564] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:57,564] [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_000187975.2	s__Streptococcus criceti	99.9952	796	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_011038795.1	s__Streptococcus sp011038795	93.3169	664	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_900459175.1	s__Streptococcus downei	80.4161	400	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.20	97.65	0.95	0.94	6	-
GCF_000686605.1	s__Streptococcus sobrinus	80.3793	390	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.93	98.60	0.95	0.92	52	-
GCF_001937065.1	s__Streptococcus sp001937065	79.295	155	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431045.1	s__Streptococcus orisasini	79.1914	181	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	78.6729	144	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_900104225.1	s__Streptococcus equinus_D	78.4212	89	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003686955.1	s__Streptococcus sp003686955	78.0879	93	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380125.1	s__Streptococcus ovis	77.8894	78	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	77.8494	114	806	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	77.7813	108	806	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 13:49:57,566] [INFO] GTDB search result was written to GCF_900459215.1_44087_A02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:57,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:57,576] [INFO] DFAST_QC result json was written to GCF_900459215.1_44087_A02_genomic.fna/dqc_result.json
[2024-01-24 13:49:57,576] [INFO] DFAST_QC completed!
[2024-01-24 13:49:57,577] [INFO] Total running time: 0h0m45s