[2024-01-24 13:55:14,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference
[2024-01-24 13:55:16,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,179] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg68069e64-a43c-4352-99a1-e1285a74ad57/GCF_014635565.1_ASM1463556v1_genomic.fna.gz | prodigal -d GCF_014635565.1_ASM1463556v1_genomic.fna/cds.fna -a GCF_014635565.1_ASM1463556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:20,064] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:20,064] [INFO] Task started: HMMsearch
[2024-01-24 13:55:20,065] [INFO] Running command: hmmsearch --tblout GCF_014635565.1_ASM1463556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/reference_markers.hmm GCF_014635565.1_ASM1463556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:20,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:20,305] [INFO] Found 6/6 markers.
[2024-01-24 13:55:20,328] [INFO] Query marker FASTA was written to GCF_014635565.1_ASM1463556v1_genomic.fna/markers.fasta
[2024-01-24 13:55:20,328] [INFO] Task started: Blastn
[2024-01-24 13:55:20,328] [INFO] Running command: blastn -query GCF_014635565.1_ASM1463556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/reference_markers.fasta -out GCF_014635565.1_ASM1463556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:20,947] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:20,951] [INFO] Selected 15 target genomes.
[2024-01-24 13:55:20,951] [INFO] Target genome list was writen to GCF_014635565.1_ASM1463556v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:20,998] [INFO] Task started: fastANI
[2024-01-24 13:55:20,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg68069e64-a43c-4352-99a1-e1285a74ad57/GCF_014635565.1_ASM1463556v1_genomic.fna.gz --refList GCF_014635565.1_ASM1463556v1_genomic.fna/target_genomes.txt --output GCF_014635565.1_ASM1463556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:27,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:27,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:27,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:27,343] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:27,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:27,344] [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
Jeotgalicoccus schoeneichii	strain=CCM 8667	GCA_014635565.1	1812261	1812261	type	True	100.0	587	587	95	conclusive
Jeotgalicoccus schoeneichii	strain=CIP 111030	GCA_903994025.1	1812261	1812261	type	True	99.9589	575	587	95	conclusive
Jeotgalicoccus pinnipedialis	strain=DSM 17030	GCA_017873645.1	110845	110845	type	True	83.9403	415	587	95	below_threshold
Jeotgalicoccus pinnipedialis	strain=CIP 107946	GCA_903994035.1	110845	110845	type	True	83.8836	405	587	95	below_threshold
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_019357495.1	489910	489910	type	True	78.5012	132	587	95	below_threshold
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_014202595.1	489910	489910	type	True	78.2912	129	587	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:27,346] [INFO] DFAST Taxonomy check result was written to GCF_014635565.1_ASM1463556v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:27,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:27,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:27,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/checkm_data
[2024-01-24 13:55:27,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:27,372] [INFO] Task started: CheckM
[2024-01-24 13:55:27,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635565.1_ASM1463556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635565.1_ASM1463556v1_genomic.fna/checkm_input GCF_014635565.1_ASM1463556v1_genomic.fna/checkm_result
[2024-01-24 13:55:46,507] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:46,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:46,526] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:46,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:46,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635565.1_ASM1463556v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:46,527] [INFO] Task started: Blastn
[2024-01-24 13:55:46,527] [INFO] Running command: blastn -query GCF_014635565.1_ASM1463556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89bf07b6-b3f4-4ecb-be0f-5c52551a3c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635565.1_ASM1463556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:47,312] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:47,320] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:47,321] [INFO] Target genome list was writen to GCF_014635565.1_ASM1463556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:47,348] [INFO] Task started: fastANI
[2024-01-24 13:55:47,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg68069e64-a43c-4352-99a1-e1285a74ad57/GCF_014635565.1_ASM1463556v1_genomic.fna.gz --refList GCF_014635565.1_ASM1463556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635565.1_ASM1463556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:56,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:56,168] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:56,168] [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_014635565.1	s__Jeotgalicoccus_A schoeneichii	100.0	587	587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_903994035.1	s__Jeotgalicoccus_A pinnipedialis	83.8836	405	587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001696685.1	s__Nosocomiicoccus ampullae_A	79.0649	135	587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.642	98.29	98.16	0.91	0.90	5	-
GCF_014202595.1	s__Nosocomiicoccus ampullae	78.2912	129	587	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:56,170] [INFO] GTDB search result was written to GCF_014635565.1_ASM1463556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:56,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:56,174] [INFO] DFAST_QC result json was written to GCF_014635565.1_ASM1463556v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:56,175] [INFO] DFAST_QC completed!
[2024-01-24 13:55:56,175] [INFO] Total running time: 0h0m41s