[2024-01-24 13:41:26,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,094] [INFO] DQC Reference Directory: /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference
[2024-01-24 13:41:27,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,505] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg146b279f-f66e-49ff-824f-603e6968cb62/GCF_003946005.1_ASM394600v1_genomic.fna.gz | prodigal -d GCF_003946005.1_ASM394600v1_genomic.fna/cds.fna -a GCF_003946005.1_ASM394600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:33,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:33,084] [INFO] Task started: HMMsearch
[2024-01-24 13:41:33,084] [INFO] Running command: hmmsearch --tblout GCF_003946005.1_ASM394600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/reference_markers.hmm GCF_003946005.1_ASM394600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:33,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:33,359] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg146b279f-f66e-49ff-824f-603e6968cb62/GCF_003946005.1_ASM394600v1_genomic.fna.gz]
[2024-01-24 13:41:33,397] [INFO] Query marker FASTA was written to GCF_003946005.1_ASM394600v1_genomic.fna/markers.fasta
[2024-01-24 13:41:33,398] [INFO] Task started: Blastn
[2024-01-24 13:41:33,398] [INFO] Running command: blastn -query GCF_003946005.1_ASM394600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/reference_markers.fasta -out GCF_003946005.1_ASM394600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:34,099] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:34,103] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:34,103] [INFO] Target genome list was writen to GCF_003946005.1_ASM394600v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:34,113] [INFO] Task started: fastANI
[2024-01-24 13:41:34,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg146b279f-f66e-49ff-824f-603e6968cb62/GCF_003946005.1_ASM394600v1_genomic.fna.gz --refList GCF_003946005.1_ASM394600v1_genomic.fna/target_genomes.txt --output GCF_003946005.1_ASM394600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:41,778] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:41,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:41,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:41,791] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:41,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:41,791] [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
Companilactobacillus allii	strain=JCM 31938	GCA_003946005.1	1847728	1847728	type	True	100.0	832	833	95	conclusive
Companilactobacillus allii	strain=WiKim39	GCA_001971585.1	1847728	1847728	type	True	99.9963	829	833	95	conclusive
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	99.992	827	833	95	conclusive
Companilactobacillus hulinensis	strain=8-1(1)	GCA_003946555.1	2486007	2486007	type	True	83.4529	534	833	95	below_threshold
Companilactobacillus nodensis	strain=DSM 19682	GCA_001435555.1	460870	460870	type	True	82.0456	428	833	95	below_threshold
Companilactobacillus jidongensis	strain=204-8	GCA_003946575.1	2486006	2486006	type	True	81.7545	461	833	95	below_threshold
Companilactobacillus insicii	strain=DSM 29801	GCA_003946015.1	1732567	1732567	type	True	81.4478	410	833	95	below_threshold
Companilactobacillus baiquanensis	strain=184-8	GCA_003946605.1	2486005	2486005	type	True	79.9273	278	833	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	79.5972	268	833	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	79.4554	203	833	95	below_threshold
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	79.2146	263	833	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	79.2017	266	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:41,795] [INFO] DFAST Taxonomy check result was written to GCF_003946005.1_ASM394600v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:41,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:41,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:41,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/checkm_data
[2024-01-24 13:41:41,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:41,827] [INFO] Task started: CheckM
[2024-01-24 13:41:41,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946005.1_ASM394600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946005.1_ASM394600v1_genomic.fna/checkm_input GCF_003946005.1_ASM394600v1_genomic.fna/checkm_result
[2024-01-24 13:42:05,482] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:05,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:05,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:05,505] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:05,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946005.1_ASM394600v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:05,506] [INFO] Task started: Blastn
[2024-01-24 13:42:05,506] [INFO] Running command: blastn -query GCF_003946005.1_ASM394600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5faeab-3578-4b93-a758-beef71101562/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946005.1_ASM394600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:06,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:06,343] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:06,343] [INFO] Target genome list was writen to GCF_003946005.1_ASM394600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:06,348] [INFO] Task started: fastANI
[2024-01-24 13:42:06,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg146b279f-f66e-49ff-824f-603e6968cb62/GCF_003946005.1_ASM394600v1_genomic.fna.gz --refList GCF_003946005.1_ASM394600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946005.1_ASM394600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:11,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,863] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:11,863] [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_001971585.1	s__Companilactobacillus allii	99.9963	829	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003946555.1	s__Companilactobacillus hulinensis	83.4697	533	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615905.1	s__Companilactobacillus nodensis	81.8756	429	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.98	99.98	1.00	1.00	3	-
GCF_003946575.1	s__Companilactobacillus jidongensis	81.7545	461	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946015.1	s__Companilactobacillus insicii	81.4485	409	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946605.1	s__Companilactobacillus baiquanensis	79.9482	278	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434665.1	s__Companilactobacillus tucceti	79.5507	286	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600985.1	s__Companilactobacillus halodurans	79.4394	238	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.75	99.75	0.93	0.93	2	-
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	79.2899	289	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCF_005404815.1	s__Companilactobacillus huachuanensis	79.2324	262	833	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,865] [INFO] GTDB search result was written to GCF_003946005.1_ASM394600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:11,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:11,870] [INFO] DFAST_QC result json was written to GCF_003946005.1_ASM394600v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:11,870] [INFO] DFAST_QC completed!
[2024-01-24 13:42:11,871] [INFO] Total running time: 0h0m46s