[2023-06-13 23:17:47,292] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:17:47,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:17:47,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference
[2023-06-13 23:17:48,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:17:48,932] [INFO] Task started: Prodigal
[2023-06-13 23:17:48,933] [INFO] Running command: gunzip -c /var/lib/cwl/stgc745e5d9-3ceb-4641-9b24-81ae4d4bc89c/GCA_022484265.1_ASM2248426v1_genomic.fna.gz | prodigal -d GCA_022484265.1_ASM2248426v1_genomic.fna/cds.fna -a GCA_022484265.1_ASM2248426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:17:54,313] [INFO] Task succeeded: Prodigal
[2023-06-13 23:17:54,314] [INFO] Task started: HMMsearch
[2023-06-13 23:17:54,314] [INFO] Running command: hmmsearch --tblout GCA_022484265.1_ASM2248426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/reference_markers.hmm GCA_022484265.1_ASM2248426v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:17:54,506] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:17:54,507] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc745e5d9-3ceb-4641-9b24-81ae4d4bc89c/GCA_022484265.1_ASM2248426v1_genomic.fna.gz]
[2023-06-13 23:17:54,529] [INFO] Query marker FASTA was written to GCA_022484265.1_ASM2248426v1_genomic.fna/markers.fasta
[2023-06-13 23:17:54,530] [INFO] Task started: Blastn
[2023-06-13 23:17:54,530] [INFO] Running command: blastn -query GCA_022484265.1_ASM2248426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/reference_markers.fasta -out GCA_022484265.1_ASM2248426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:17:55,065] [INFO] Task succeeded: Blastn
[2023-06-13 23:17:55,068] [INFO] Selected 15 target genomes.
[2023-06-13 23:17:55,069] [INFO] Target genome list was writen to GCA_022484265.1_ASM2248426v1_genomic.fna/target_genomes.txt
[2023-06-13 23:17:55,069] [INFO] Task started: fastANI
[2023-06-13 23:17:55,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgc745e5d9-3ceb-4641-9b24-81ae4d4bc89c/GCA_022484265.1_ASM2248426v1_genomic.fna.gz --refList GCA_022484265.1_ASM2248426v1_genomic.fna/target_genomes.txt --output GCA_022484265.1_ASM2248426v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:18:02,218] [INFO] Task succeeded: fastANI
[2023-06-13 23:18:02,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:18:02,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:18:02,228] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:18:02,228] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 23:18:02,228] [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 ginsenosidimutans	strain=EMML 3041	GCA_001050475.1	1007676	1007676	type	True	81.8068	443	888	95	below_threshold
Companilactobacillus zhongbaensis	strain=M1575	GCA_003946515.1	2486009	2486009	type	True	81.0645	446	888	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	80.9049	346	888	95	below_threshold
Companilactobacillus furfuricola	strain=JCM 18764	GCA_003946325.1	1462575	1462575	type	True	80.5265	416	888	95	below_threshold
Companilactobacillus versmoldensis	strain=KCTC 3814	GCA_000260455.1	194326	194326	type	True	80.4434	390	888	95	below_threshold
Companilactobacillus versmoldensis	strain=DSM 14857	GCA_001434295.1	194326	194326	type	True	80.2913	397	888	95	below_threshold
Companilactobacillus insicii	strain=DSM 29801	GCA_003946015.1	1732567	1732567	type	True	79.2021	180	888	95	below_threshold
Companilactobacillus baiquanensis	strain=184-8	GCA_003946605.1	2486005	2486005	type	True	78.988	207	888	95	below_threshold
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	78.8477	215	888	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	78.8129	194	888	95	below_threshold
Companilactobacillus suantsaicola	strain=BCRC 81127	GCA_004745525.1	2487723	2487723	type	True	78.7475	201	888	95	below_threshold
Companilactobacillus futsaii	strain=JCM 17355	GCA_001435505.1	938155	938155	type	True	78.4844	198	888	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:18:02,230] [INFO] DFAST Taxonomy check result was written to GCA_022484265.1_ASM2248426v1_genomic.fna/tc_result.tsv
[2023-06-13 23:18:02,231] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:18:02,231] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:18:02,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/checkm_data
[2023-06-13 23:18:02,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:18:02,261] [INFO] Task started: CheckM
[2023-06-13 23:18:02,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022484265.1_ASM2248426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022484265.1_ASM2248426v1_genomic.fna/checkm_input GCA_022484265.1_ASM2248426v1_genomic.fna/checkm_result
[2023-06-13 23:18:23,978] [INFO] Task succeeded: CheckM
[2023-06-13 23:18:23,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:18:23,997] [INFO] ===== Completeness check finished =====
[2023-06-13 23:18:23,997] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:18:23,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022484265.1_ASM2248426v1_genomic.fna/markers.fasta)
[2023-06-13 23:18:23,999] [INFO] Task started: Blastn
[2023-06-13 23:18:23,999] [INFO] Running command: blastn -query GCA_022484265.1_ASM2248426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07fa0a27-335d-4aa6-9a87-210a99a7333e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022484265.1_ASM2248426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:18:24,718] [INFO] Task succeeded: Blastn
[2023-06-13 23:18:24,722] [INFO] Selected 13 target genomes.
[2023-06-13 23:18:24,722] [INFO] Target genome list was writen to GCA_022484265.1_ASM2248426v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:18:24,723] [INFO] Task started: fastANI
[2023-06-13 23:18:24,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgc745e5d9-3ceb-4641-9b24-81ae4d4bc89c/GCA_022484265.1_ASM2248426v1_genomic.fna.gz --refList GCA_022484265.1_ASM2248426v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022484265.1_ASM2248426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:18:31,398] [INFO] Task succeeded: fastANI
[2023-06-13 23:18:31,407] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:18:31,407] [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_001050475.1	s__Companilactobacillus ginsenosidimutans	81.8292	442	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946515.1	s__Companilactobacillus zhongbaensis	81.0559	446	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946505.1	s__Companilactobacillus mishanensis	80.8802	347	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.34	97.53	0.96	0.93	4	-
GCF_003946325.1	s__Companilactobacillus furfuricola	80.523	417	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434295.1	s__Companilactobacillus versmoldensis	80.2913	397	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003946015.1	s__Companilactobacillus insicii	79.2021	180	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003606365.2	s__Companilactobacillus zhachilii	79.1583	216	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_005405305.1	s__Companilactobacillus formosensis	78.989	207	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014058425.1	s__Companilactobacillus pabuli	78.8747	213	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	78.7583	202	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434985.1	s__Companilactobacillus paralimentarius	78.6319	178	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.97	99.96	0.99	0.99	4	-
GCF_001435505.1	s__Companilactobacillus futsaii	78.4844	198	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCA_019116025.1	s__Companilactobacillus pullicola	78.1603	188	888	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:18:31,409] [INFO] GTDB search result was written to GCA_022484265.1_ASM2248426v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:18:31,409] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:18:31,412] [INFO] DFAST_QC result json was written to GCA_022484265.1_ASM2248426v1_genomic.fna/dqc_result.json
[2023-06-13 23:18:31,413] [INFO] DFAST_QC completed!
[2023-06-13 23:18:31,413] [INFO] Total running time: 0h0m44s