[2024-01-24 13:40:55,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference
[2024-01-24 13:40:56,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,589] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg8735a66c-ad97-4c01-a5a6-e274ffac7106/GCF_007989385.1_ASM798938v1_genomic.fna.gz | prodigal -d GCF_007989385.1_ASM798938v1_genomic.fna/cds.fna -a GCF_007989385.1_ASM798938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,453] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,453] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,453] [INFO] Running command: hmmsearch --tblout GCF_007989385.1_ASM798938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/reference_markers.hmm GCF_007989385.1_ASM798938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,733] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,772] [INFO] Query marker FASTA was written to GCF_007989385.1_ASM798938v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,772] [INFO] Task started: Blastn
[2024-01-24 13:41:00,772] [INFO] Running command: blastn -query GCF_007989385.1_ASM798938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/reference_markers.fasta -out GCF_007989385.1_ASM798938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,337] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:01,337] [INFO] Target genome list was writen to GCF_007989385.1_ASM798938v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,349] [INFO] Task started: fastANI
[2024-01-24 13:41:01,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg8735a66c-ad97-4c01-a5a6-e274ffac7106/GCF_007989385.1_ASM798938v1_genomic.fna.gz --refList GCF_007989385.1_ASM798938v1_genomic.fna/target_genomes.txt --output GCF_007989385.1_ASM798938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:07,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:07,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:07,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,664] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:07,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:07,665] [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=NBRC 100002	GCA_007989385.1	191770	191770	type	True	100.0	798	801	95	conclusive
Marinilactibacillus psychrotolerans	strain=M13-2T	GCA_019650195.1	191770	191770	type	True	99.9801	801	801	95	conclusive
Marinilactibacillus psychrotolerans	strain=DSM 19582	GCA_900101525.1	191770	191770	type	True	99.9748	796	801	95	conclusive
Marinilactibacillus piezotolerans	strain=DSM 16108	GCA_900114235.1	258723	258723	type	True	87.9868	586	801	95	below_threshold
Alkalibacterium putridalgicola	strain=DSM 19182	GCA_900109825.1	426703	426703	type	True	78.4624	54	801	95	below_threshold
Alkalibacterium gilvum	strain=DSM 25751	GCA_900109085.1	1130080	1130080	type	True	77.2429	57	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,666] [INFO] DFAST Taxonomy check result was written to GCF_007989385.1_ASM798938v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/checkm_data
[2024-01-24 13:41:07,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,695] [INFO] Task started: CheckM
[2024-01-24 13:41:07,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989385.1_ASM798938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989385.1_ASM798938v1_genomic.fna/checkm_input GCF_007989385.1_ASM798938v1_genomic.fna/checkm_result
[2024-01-24 13:41:25,809] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:25,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,825] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:25,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:25,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989385.1_ASM798938v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:25,826] [INFO] Task started: Blastn
[2024-01-24 13:41:25,826] [INFO] Running command: blastn -query GCF_007989385.1_ASM798938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg682736fe-256c-478f-a98a-a5010eb56109/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989385.1_ASM798938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:26,577] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:26,580] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:26,580] [INFO] Target genome list was writen to GCF_007989385.1_ASM798938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:26,590] [INFO] Task started: fastANI
[2024-01-24 13:41:26,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg8735a66c-ad97-4c01-a5a6-e274ffac7106/GCF_007989385.1_ASM798938v1_genomic.fna.gz --refList GCF_007989385.1_ASM798938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989385.1_ASM798938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:34,372] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:34,379] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:34,379] [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	99.9748	796	801	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	87.9824	586	801	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	79.2568	213	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599325.1	s__Marinilactibacillus sp017599325	78.729	250	801	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	78.4624	54	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001885615.1	s__Alkalibacterium sp001885615	77.3084	61	801	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	77.2429	57	801	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	76.6244	58	801	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 13:41:34,380] [INFO] GTDB search result was written to GCF_007989385.1_ASM798938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:34,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:34,383] [INFO] DFAST_QC result json was written to GCF_007989385.1_ASM798938v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:34,383] [INFO] DFAST_QC completed!
[2024-01-24 13:41:34,383] [INFO] Total running time: 0h0m39s