[2024-01-24 11:44:23,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stga51526b5-57f6-4711-ab16-fbd1d67b8e74/GCF_007988845.1_ASM798884v1_genomic.fna.gz | prodigal -d GCF_007988845.1_ASM798884v1_genomic.fna/cds.fna -a GCF_007988845.1_ASM798884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:32,031] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:32,031] [INFO] Task started: HMMsearch
[2024-01-24 11:44:32,031] [INFO] Running command: hmmsearch --tblout GCF_007988845.1_ASM798884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/reference_markers.hmm GCF_007988845.1_ASM798884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:32,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:32,264] [INFO] Found 6/6 markers.
[2024-01-24 11:44:32,290] [INFO] Query marker FASTA was written to GCF_007988845.1_ASM798884v1_genomic.fna/markers.fasta
[2024-01-24 11:44:32,291] [INFO] Task started: Blastn
[2024-01-24 11:44:32,291] [INFO] Running command: blastn -query GCF_007988845.1_ASM798884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/reference_markers.fasta -out GCF_007988845.1_ASM798884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:32,867] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:32,870] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:32,870] [INFO] Target genome list was writen to GCF_007988845.1_ASM798884v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:32,897] [INFO] Task started: fastANI
[2024-01-24 11:44:32,897] [INFO] Running command: fastANI --query /var/lib/cwl/stga51526b5-57f6-4711-ab16-fbd1d67b8e74/GCF_007988845.1_ASM798884v1_genomic.fna.gz --refList GCF_007988845.1_ASM798884v1_genomic.fna/target_genomes.txt --output GCF_007988845.1_ASM798884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:42,504] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:42,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:42,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:42,514] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:42,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:42,514] [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
Alkalibacterium putridalgicola	strain=NBRC 103243	GCA_007988845.1	426703	426703	type	True	100.0	827	831	95	conclusive
Alkalibacterium putridalgicola	strain=DSM 19182	GCA_900109825.1	426703	426703	type	True	99.9828	819	831	95	conclusive
Alkalibacterium subtropicum	strain=DSM 23664	GCA_900112455.1	753702	753702	type	True	86.6189	651	831	95	below_threshold
Alkalibacterium kapii	strain=NBRC 103247	GCA_007988865.1	426704	426704	type	True	79.7832	266	831	95	below_threshold
Alkalibacterium gilvum	strain=DSM 25751	GCA_900109085.1	1130080	1130080	type	True	79.4462	221	831	95	below_threshold
Alkalibacterium pelagium	strain=NBRC 103242	GCA_007991315.1	426702	426702	type	True	78.8868	146	831	95	below_threshold
Alkalibacterium pelagium	strain=DSM 19183	GCA_900109325.1	426702	426702	type	True	78.681	153	831	95	below_threshold
Alkalibacterium olivapovliticus	strain=DSM 13175	GCA_003003275.1	99907	99907	type	True	78.5741	142	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,516] [INFO] DFAST Taxonomy check result was written to GCF_007988845.1_ASM798884v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:42,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:42,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:42,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/checkm_data
[2024-01-24 11:44:42,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:42,544] [INFO] Task started: CheckM
[2024-01-24 11:44:42,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007988845.1_ASM798884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007988845.1_ASM798884v1_genomic.fna/checkm_input GCF_007988845.1_ASM798884v1_genomic.fna/checkm_result
[2024-01-24 11:45:06,815] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:06,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:06,840] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:06,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:06,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007988845.1_ASM798884v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:06,842] [INFO] Task started: Blastn
[2024-01-24 11:45:06,842] [INFO] Running command: blastn -query GCF_007988845.1_ASM798884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb933fc-10bc-4b5d-8b99-e80aeb27ee93/dqc_reference/reference_markers_gtdb.fasta -out GCF_007988845.1_ASM798884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:07,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:07,665] [INFO] Selected 18 target genomes.
[2024-01-24 11:45:07,666] [INFO] Target genome list was writen to GCF_007988845.1_ASM798884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:07,682] [INFO] Task started: fastANI
[2024-01-24 11:45:07,682] [INFO] Running command: fastANI --query /var/lib/cwl/stga51526b5-57f6-4711-ab16-fbd1d67b8e74/GCF_007988845.1_ASM798884v1_genomic.fna.gz --refList GCF_007988845.1_ASM798884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007988845.1_ASM798884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:15,959] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:15,975] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:15,976] [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_900109825.1	s__Alkalibacterium putridalgicola	99.9828	819	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_900112455.1	s__Alkalibacterium subtropicum	86.6369	650	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988865.1	s__Alkalibacterium kapii	79.7832	266	831	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	79.449	220	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.35	99.35	0.91	0.91	2	-
GCF_900101165.1	s__Alkalibacterium thalassium	78.7362	126	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109325.1	s__Alkalibacterium pelagium	78.6816	153	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003003275.1	s__Alkalibacterium olivapovliticus	78.5631	143	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885615.1	s__Alkalibacterium sp001885615	78.386	294	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692455.1	s__Alkalibacterium sp007692455	77.9423	126	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599325.1	s__Marinilactibacillus sp017599325	77.7212	58	831	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:15,978] [INFO] GTDB search result was written to GCF_007988845.1_ASM798884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:15,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:15,981] [INFO] DFAST_QC result json was written to GCF_007988845.1_ASM798884v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:15,981] [INFO] DFAST_QC completed!
[2024-01-24 11:45:15,982] [INFO] Total running time: 0h0m52s