[2024-01-24 14:22:30,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:30,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:30,912] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference
[2024-01-24 14:22:32,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:32,228] [INFO] Task started: Prodigal
[2024-01-24 14:22:32,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbf928d-9f32-4405-b4ab-d3f36c4207e2/GCF_014202595.1_ASM1420259v1_genomic.fna.gz | prodigal -d GCF_014202595.1_ASM1420259v1_genomic.fna/cds.fna -a GCF_014202595.1_ASM1420259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:35,000] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:35,001] [INFO] Task started: HMMsearch
[2024-01-24 14:22:35,001] [INFO] Running command: hmmsearch --tblout GCF_014202595.1_ASM1420259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/reference_markers.hmm GCF_014202595.1_ASM1420259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:35,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:35,257] [INFO] Found 6/6 markers.
[2024-01-24 14:22:35,281] [INFO] Query marker FASTA was written to GCF_014202595.1_ASM1420259v1_genomic.fna/markers.fasta
[2024-01-24 14:22:35,282] [INFO] Task started: Blastn
[2024-01-24 14:22:35,283] [INFO] Running command: blastn -query GCF_014202595.1_ASM1420259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/reference_markers.fasta -out GCF_014202595.1_ASM1420259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:35,976] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:35,980] [INFO] Selected 17 target genomes.
[2024-01-24 14:22:35,981] [INFO] Target genome list was writen to GCF_014202595.1_ASM1420259v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:35,991] [INFO] Task started: fastANI
[2024-01-24 14:22:35,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf928d-9f32-4405-b4ab-d3f36c4207e2/GCF_014202595.1_ASM1420259v1_genomic.fna.gz --refList GCF_014202595.1_ASM1420259v1_genomic.fna/target_genomes.txt --output GCF_014202595.1_ASM1420259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:43,371] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:43,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:43,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:43,384] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:43,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:43,384] [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
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_014202595.1	489910	489910	type	True	100.0	498	500	95	conclusive
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_019357495.1	489910	489910	type	True	99.9984	499	500	95	conclusive
Nosocomiicoccus massiliensis	strain=NP2	GCA_000438455.1	1232430	1232430	type	True	82.0762	307	500	95	below_threshold
Jeotgalicoccus schoeneichii	strain=CIP 111030	GCA_903994025.1	1812261	1812261	type	True	78.4056	128	500	95	below_threshold
Jeotgalicoccus schoeneichii	strain=CCM 8667	GCA_014635565.1	1812261	1812261	type	True	78.3609	130	500	95	below_threshold
Aliicoccus persicus	strain=IBRC-M10081	GCA_900110815.1	930138	930138	type	True	77.4995	51	500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:43,386] [INFO] DFAST Taxonomy check result was written to GCF_014202595.1_ASM1420259v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:43,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:43,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:43,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/checkm_data
[2024-01-24 14:22:43,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:43,405] [INFO] Task started: CheckM
[2024-01-24 14:22:43,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202595.1_ASM1420259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202595.1_ASM1420259v1_genomic.fna/checkm_input GCF_014202595.1_ASM1420259v1_genomic.fna/checkm_result
[2024-01-24 14:23:01,931] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:01,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:01,957] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:01,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:01,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202595.1_ASM1420259v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:01,958] [INFO] Task started: Blastn
[2024-01-24 14:23:01,958] [INFO] Running command: blastn -query GCF_014202595.1_ASM1420259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8769d66-09c3-4e13-992c-b14d8d899c8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202595.1_ASM1420259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:03,151] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:03,154] [INFO] Selected 12 target genomes.
[2024-01-24 14:23:03,154] [INFO] Target genome list was writen to GCF_014202595.1_ASM1420259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:03,165] [INFO] Task started: fastANI
[2024-01-24 14:23:03,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf928d-9f32-4405-b4ab-d3f36c4207e2/GCF_014202595.1_ASM1420259v1_genomic.fna.gz --refList GCF_014202595.1_ASM1420259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202595.1_ASM1420259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:08,175] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:08,186] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:08,187] [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_014202595.1	s__Nosocomiicoccus ampullae	100.0	498	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019119225.1	s__Nosocomiicoccus stercorigallinarum	94.4339	393	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696685.1	s__Nosocomiicoccus ampullae_A	82.4495	372	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.642	98.29	98.16	0.91	0.90	5	-
GCF_000438455.1	s__Nosocomiicoccus massiliensis	82.0675	307	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.642	100.00	100.00	0.99	0.99	2	-
GCF_014635565.1	s__Jeotgalicoccus_A schoeneichii	78.3326	131	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900110815.1	s__Aliicoccus persicus	77.5597	50	500	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Aliicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,193] [INFO] GTDB search result was written to GCF_014202595.1_ASM1420259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:08,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:08,197] [INFO] DFAST_QC result json was written to GCF_014202595.1_ASM1420259v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:08,197] [INFO] DFAST_QC completed!
[2024-01-24 14:23:08,197] [INFO] Total running time: 0h0m37s