[2024-01-24 14:31:28,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference
[2024-01-24 14:31:30,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:30,049] [INFO] Task started: Prodigal
[2024-01-24 14:31:30,049] [INFO] Running command: gunzip -c /var/lib/cwl/stg37672e66-b83e-496c-ad60-51b245d7c244/GCF_006370295.1_ASM637029v1_genomic.fna.gz | prodigal -d GCF_006370295.1_ASM637029v1_genomic.fna/cds.fna -a GCF_006370295.1_ASM637029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:38,107] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:38,107] [INFO] Task started: HMMsearch
[2024-01-24 14:31:38,107] [INFO] Running command: hmmsearch --tblout GCF_006370295.1_ASM637029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/reference_markers.hmm GCF_006370295.1_ASM637029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:38,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:38,319] [INFO] Found 6/6 markers.
[2024-01-24 14:31:38,342] [INFO] Query marker FASTA was written to GCF_006370295.1_ASM637029v1_genomic.fna/markers.fasta
[2024-01-24 14:31:38,342] [INFO] Task started: Blastn
[2024-01-24 14:31:38,342] [INFO] Running command: blastn -query GCF_006370295.1_ASM637029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/reference_markers.fasta -out GCF_006370295.1_ASM637029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:38,877] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:38,879] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:38,880] [INFO] Target genome list was writen to GCF_006370295.1_ASM637029v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:38,903] [INFO] Task started: fastANI
[2024-01-24 14:31:38,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg37672e66-b83e-496c-ad60-51b245d7c244/GCF_006370295.1_ASM637029v1_genomic.fna.gz --refList GCF_006370295.1_ASM637029v1_genomic.fna/target_genomes.txt --output GCF_006370295.1_ASM637029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:45,542] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:45,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:45,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:45,549] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:45,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:45,549] [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
Trichococcus shcherbakoviae subsp. psychrophilus	strain=SKBG	GCA_006370295.1	2585775	2094020	type	True	100.0	1019	1040	95	conclusive
Trichococcus alkaliphilus	strain=B5	GCA_003008695.1	2052943	2052943	type	True	92.4262	810	1040	95	below_threshold
Trichococcus pasteurii	strain=DSM 2381	GCA_900112935.1	43064	43064	type	True	91.8165	837	1040	95	below_threshold
Trichococcus paludicola	strain=B7-2	GCA_003052295.1	2052942	2052942	type	True	91.7634	572	1040	95	below_threshold
Trichococcus collinsii	strain=DSM 14526	GCA_900107505.1	157076	157076	type	True	91.1532	836	1040	95	below_threshold
Trichococcus patagoniensis	strain=DSM 18806	GCA_003051085.1	382641	382641	type	True	90.7655	805	1040	95	below_threshold
Trichococcus flocculiformis	strain=DSM 2094	GCA_900113645.1	82803	82803	type	True	89.8679	710	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,550] [INFO] DFAST Taxonomy check result was written to GCF_006370295.1_ASM637029v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:45,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:45,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:45,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/checkm_data
[2024-01-24 14:31:45,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:45,584] [INFO] Task started: CheckM
[2024-01-24 14:31:45,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006370295.1_ASM637029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006370295.1_ASM637029v1_genomic.fna/checkm_input GCF_006370295.1_ASM637029v1_genomic.fna/checkm_result
[2024-01-24 14:32:13,903] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:13,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:13,920] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:13,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:13,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006370295.1_ASM637029v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:13,921] [INFO] Task started: Blastn
[2024-01-24 14:32:13,922] [INFO] Running command: blastn -query GCF_006370295.1_ASM637029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70deb25c-d535-45dc-b7ce-b18e8ff4b37c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006370295.1_ASM637029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:14,679] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:14,683] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:14,683] [INFO] Target genome list was writen to GCF_006370295.1_ASM637029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:14,687] [INFO] Task started: fastANI
[2024-01-24 14:32:14,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg37672e66-b83e-496c-ad60-51b245d7c244/GCF_006370295.1_ASM637029v1_genomic.fna.gz --refList GCF_006370295.1_ASM637029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006370295.1_ASM637029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:20,217] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:20,222] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:20,222] [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
GCA_002155105.1	s__Trichococcus shcherbakoviae	97.7684	897	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	97.18	96.59	0.87	0.86	3	conclusive
GCF_003008695.1	s__Trichococcus alkaliphilus	92.4262	810	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112935.1	s__Trichococcus pasteurii	91.8373	836	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_003052295.1	s__Trichococcus paludicola	91.7634	572	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107505.1	s__Trichococcus collinsii	91.1532	836	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003051085.1	s__Trichococcus patagoniensis	90.7856	804	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113645.1	s__Trichococcus flocculiformis	89.8894	709	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	98.05	95.30	0.92	0.79	15	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,224] [INFO] GTDB search result was written to GCF_006370295.1_ASM637029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:20,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:20,226] [INFO] DFAST_QC result json was written to GCF_006370295.1_ASM637029v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:20,226] [INFO] DFAST_QC completed!
[2024-01-24 14:32:20,226] [INFO] Total running time: 0h0m51s