[2024-01-24 12:09:05,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference
[2024-01-24 12:09:06,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,491] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgd157821e-0940-4df1-8961-18bd4ee00336/GCF_019650195.1_ASM1965019v1_genomic.fna.gz | prodigal -d GCF_019650195.1_ASM1965019v1_genomic.fna/cds.fna -a GCF_019650195.1_ASM1965019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:11,021] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:11,021] [INFO] Task started: HMMsearch
[2024-01-24 12:09:11,021] [INFO] Running command: hmmsearch --tblout GCF_019650195.1_ASM1965019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/reference_markers.hmm GCF_019650195.1_ASM1965019v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:11,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:11,266] [INFO] Found 6/6 markers.
[2024-01-24 12:09:11,290] [INFO] Query marker FASTA was written to GCF_019650195.1_ASM1965019v1_genomic.fna/markers.fasta
[2024-01-24 12:09:11,290] [INFO] Task started: Blastn
[2024-01-24 12:09:11,290] [INFO] Running command: blastn -query GCF_019650195.1_ASM1965019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/reference_markers.fasta -out GCF_019650195.1_ASM1965019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:11,883] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:11,887] [INFO] Selected 14 target genomes.
[2024-01-24 12:09:11,888] [INFO] Target genome list was writen to GCF_019650195.1_ASM1965019v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:11,895] [INFO] Task started: fastANI
[2024-01-24 12:09:11,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgd157821e-0940-4df1-8961-18bd4ee00336/GCF_019650195.1_ASM1965019v1_genomic.fna.gz --refList GCF_019650195.1_ASM1965019v1_genomic.fna/target_genomes.txt --output GCF_019650195.1_ASM1965019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:18,353] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:18,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:18,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:18,363] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:09:18,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:18,363] [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
Marinilactibacillus psychrotolerans	strain=M13-2T	GCA_019650195.1	191770	191770	type	True	100.0	807	811	95	conclusive
Marinilactibacillus psychrotolerans	strain=NBRC 100002	GCA_007989385.1	191770	191770	type	True	99.9848	786	811	95	conclusive
Marinilactibacillus psychrotolerans	strain=DSM 19582	GCA_900101525.1	191770	191770	type	True	99.9799	795	811	95	conclusive
Marinilactibacillus piezotolerans	strain=DSM 16108	GCA_900114235.1	258723	258723	type	True	87.8772	600	811	95	below_threshold
Alkalibacterium putridalgicola	strain=DSM 19182	GCA_900109825.1	426703	426703	type	True	79.0694	54	811	95	below_threshold
Alkalibacterium gilvum	strain=DSM 25751	GCA_900109085.1	1130080	1130080	type	True	77.213	60	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:18,365] [INFO] DFAST Taxonomy check result was written to GCF_019650195.1_ASM1965019v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:18,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:18,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:18,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/checkm_data
[2024-01-24 12:09:18,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:18,395] [INFO] Task started: CheckM
[2024-01-24 12:09:18,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019650195.1_ASM1965019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019650195.1_ASM1965019v1_genomic.fna/checkm_input GCF_019650195.1_ASM1965019v1_genomic.fna/checkm_result
[2024-01-24 12:09:39,170] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:39,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:39,187] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:39,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:39,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019650195.1_ASM1965019v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:39,188] [INFO] Task started: Blastn
[2024-01-24 12:09:39,188] [INFO] Running command: blastn -query GCF_019650195.1_ASM1965019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05fc8e45-1170-4711-a405-44bea568470a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019650195.1_ASM1965019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:39,938] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:39,942] [INFO] Selected 19 target genomes.
[2024-01-24 12:09:39,942] [INFO] Target genome list was writen to GCF_019650195.1_ASM1965019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:39,957] [INFO] Task started: fastANI
[2024-01-24 12:09:39,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgd157821e-0940-4df1-8961-18bd4ee00336/GCF_019650195.1_ASM1965019v1_genomic.fna.gz --refList GCF_019650195.1_ASM1965019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019650195.1_ASM1965019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:47,541] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:47,553] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:47,553] [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_900101525.1	s__Marinilactibacillus psychrotolerans	99.9799	795	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	98.27	97.67	0.87	0.82	5	conclusive
GCF_900114235.1	s__Marinilactibacillus piezotolerans	87.8815	600	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	98.31	98.31	0.90	0.90	2	-
GCF_900169305.1	s__Marinilactibacillus piezotolerans_A	79.2997	211	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109825.1	s__Alkalibacterium putridalgicola	79.0694	54	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_017599325.1	s__Marinilactibacillus sp017599325	78.9493	240	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885615.1	s__Alkalibacterium sp001885615	77.4047	64	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109085.1	s__Alkalibacterium gilvum	77.213	60	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.35	99.35	0.91	0.91	2	-
GCF_000746825.1	s__Carnobacterium_A inhibens	76.8058	52	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:47,555] [INFO] GTDB search result was written to GCF_019650195.1_ASM1965019v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:47,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:47,558] [INFO] DFAST_QC result json was written to GCF_019650195.1_ASM1965019v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:47,559] [INFO] DFAST_QC completed!
[2024-01-24 12:09:47,559] [INFO] Total running time: 0h0m42s