[2024-01-24 14:55:25,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:25,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:25,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference
[2024-01-24 14:55:26,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:26,459] [INFO] Task started: Prodigal
[2024-01-24 14:55:26,459] [INFO] Running command: gunzip -c /var/lib/cwl/stge328e068-b0d1-4f8a-887f-815e3bd25aad/GCF_016026975.1_ASM1602697v1_genomic.fna.gz | prodigal -d GCF_016026975.1_ASM1602697v1_genomic.fna/cds.fna -a GCF_016026975.1_ASM1602697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:30,959] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:30,959] [INFO] Task started: HMMsearch
[2024-01-24 14:55:30,959] [INFO] Running command: hmmsearch --tblout GCF_016026975.1_ASM1602697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/reference_markers.hmm GCF_016026975.1_ASM1602697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:31,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:31,163] [INFO] Found 6/6 markers.
[2024-01-24 14:55:31,191] [INFO] Query marker FASTA was written to GCF_016026975.1_ASM1602697v1_genomic.fna/markers.fasta
[2024-01-24 14:55:31,192] [INFO] Task started: Blastn
[2024-01-24 14:55:31,192] [INFO] Running command: blastn -query GCF_016026975.1_ASM1602697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/reference_markers.fasta -out GCF_016026975.1_ASM1602697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:31,830] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:31,834] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:31,834] [INFO] Target genome list was writen to GCF_016026975.1_ASM1602697v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:31,878] [INFO] Task started: fastANI
[2024-01-24 14:55:31,878] [INFO] Running command: fastANI --query /var/lib/cwl/stge328e068-b0d1-4f8a-887f-815e3bd25aad/GCF_016026975.1_ASM1602697v1_genomic.fna.gz --refList GCF_016026975.1_ASM1602697v1_genomic.fna/target_genomes.txt --output GCF_016026975.1_ASM1602697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:37,027] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:37,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:37,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:37,034] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:55:37,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:37,035] [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
Aerococcus urinae	strain=FDAARGOS_911	GCA_016026975.1	1376	1376	suspected-type	True	100.0	658	658	95	conclusive
Aerococcus urinae	strain=CCUG36881	GCA_001543175.1	1376	1376	suspected-type	True	99.9953	658	658	95	conclusive
Aerococcus urinae	strain=NBRC 15544	GCA_001544335.1	1376	1376	suspected-type	True	99.9386	637	658	95	conclusive
Aerococcus urinae	strain=ATCC 51268	GCA_002087935.1	1376	1376	suspected-type	True	99.9373	640	658	95	conclusive
Aerococcus sanguinicola	strain=CCUG43001	GCA_001543145.1	119206	119206	type	True	80.7048	68	658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:37,036] [INFO] DFAST Taxonomy check result was written to GCF_016026975.1_ASM1602697v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:37,037] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:37,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:37,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/checkm_data
[2024-01-24 14:55:37,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:37,060] [INFO] Task started: CheckM
[2024-01-24 14:55:37,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016026975.1_ASM1602697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016026975.1_ASM1602697v1_genomic.fna/checkm_input GCF_016026975.1_ASM1602697v1_genomic.fna/checkm_result
[2024-01-24 14:55:56,551] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:56,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,569] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:56,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:56,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016026975.1_ASM1602697v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:56,570] [INFO] Task started: Blastn
[2024-01-24 14:55:56,570] [INFO] Running command: blastn -query GCF_016026975.1_ASM1602697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg335e47b4-2067-4ae4-a693-0b3a2fe409df/dqc_reference/reference_markers_gtdb.fasta -out GCF_016026975.1_ASM1602697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:57,324] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:57,328] [INFO] Selected 5 target genomes.
[2024-01-24 14:55:57,328] [INFO] Target genome list was writen to GCF_016026975.1_ASM1602697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:57,332] [INFO] Task started: fastANI
[2024-01-24 14:55:57,332] [INFO] Running command: fastANI --query /var/lib/cwl/stge328e068-b0d1-4f8a-887f-815e3bd25aad/GCF_016026975.1_ASM1602697v1_genomic.fna.gz --refList GCF_016026975.1_ASM1602697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016026975.1_ASM1602697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:00,933] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:00,939] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:00,939] [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_001543175.1	s__Aerococcus urinae	99.9953	658	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	99.97	99.95	1.00	0.96	26	conclusive
GCF_003286645.1	s__Aerococcus urinae_C	93.7339	574	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	97.75	95.19	0.93	0.86	15	-
GCF_000193205.1	s__Aerococcus urinae_A	92.438	577	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002884575.1	s__Aerococcus urinae_D	92.3359	585	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	99.27	96.37	0.95	0.88	29	-
GCF_003286825.1	s__Aerococcus urinae_B	91.8481	567	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	99.01	98.40	0.96	0.94	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,941] [INFO] GTDB search result was written to GCF_016026975.1_ASM1602697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:00,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:00,944] [INFO] DFAST_QC result json was written to GCF_016026975.1_ASM1602697v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:00,944] [INFO] DFAST_QC completed!
[2024-01-24 14:56:00,944] [INFO] Total running time: 0h0m36s