[2024-01-24 12:07:06,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,924] [INFO] DQC Reference Directory: /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference
[2024-01-24 12:07:08,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,165] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,166] [INFO] Running command: gunzip -c /var/lib/cwl/stgf381416e-3719-4c58-8aa1-fa62e8aab23c/GCF_023923085.1_ASM2392308v1_genomic.fna.gz | prodigal -d GCF_023923085.1_ASM2392308v1_genomic.fna/cds.fna -a GCF_023923085.1_ASM2392308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:13,585] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:13,586] [INFO] Task started: HMMsearch
[2024-01-24 12:07:13,586] [INFO] Running command: hmmsearch --tblout GCF_023923085.1_ASM2392308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/reference_markers.hmm GCF_023923085.1_ASM2392308v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:13,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:13,839] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf381416e-3719-4c58-8aa1-fa62e8aab23c/GCF_023923085.1_ASM2392308v1_genomic.fna.gz]
[2024-01-24 12:07:13,866] [INFO] Query marker FASTA was written to GCF_023923085.1_ASM2392308v1_genomic.fna/markers.fasta
[2024-01-24 12:07:13,866] [INFO] Task started: Blastn
[2024-01-24 12:07:13,866] [INFO] Running command: blastn -query GCF_023923085.1_ASM2392308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/reference_markers.fasta -out GCF_023923085.1_ASM2392308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:14,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:14,476] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:14,477] [INFO] Target genome list was writen to GCF_023923085.1_ASM2392308v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:14,481] [INFO] Task started: fastANI
[2024-01-24 12:07:14,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf381416e-3719-4c58-8aa1-fa62e8aab23c/GCF_023923085.1_ASM2392308v1_genomic.fna.gz --refList GCF_023923085.1_ASM2392308v1_genomic.fna/target_genomes.txt --output GCF_023923085.1_ASM2392308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:21,444] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:21,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:21,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:21,458] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:07:21,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:21,458] [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=WiKim39	GCA_023923085.1	1847728	1847728	type	True	100.0	849	851	95	conclusive
Companilactobacillus allii	strain=WiKim39	GCA_001971585.1	1847728	1847728	type	True	99.9798	843	851	95	conclusive
Companilactobacillus allii	strain=JCM 31938	GCA_003946005.1	1847728	1847728	type	True	99.9569	829	851	95	conclusive
Companilactobacillus hulinensis	strain=8-1(1)	GCA_003946555.1	2486007	2486007	type	True	83.6435	525	851	95	below_threshold
Companilactobacillus nodensis	strain=DSM 19682	GCA_001435555.1	460870	460870	type	True	81.9624	429	851	95	below_threshold
Companilactobacillus jidongensis	strain=204-8	GCA_003946575.1	2486006	2486006	type	True	81.9028	448	851	95	below_threshold
Companilactobacillus insicii	strain=DSM 29801	GCA_003946015.1	1732567	1732567	type	True	81.4606	415	851	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	79.6812	277	851	95	below_threshold
Companilactobacillus baiquanensis	strain=184-8	GCA_003946605.1	2486005	2486005	type	True	79.633	287	851	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	79.4155	264	851	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	79.1427	202	851	95	below_threshold
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	79.0961	262	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:21,460] [INFO] DFAST Taxonomy check result was written to GCF_023923085.1_ASM2392308v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:21,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:21,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:21,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/checkm_data
[2024-01-24 12:07:21,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:21,487] [INFO] Task started: CheckM
[2024-01-24 12:07:21,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023923085.1_ASM2392308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023923085.1_ASM2392308v1_genomic.fna/checkm_input GCF_023923085.1_ASM2392308v1_genomic.fna/checkm_result
[2024-01-24 12:07:44,917] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:44,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,944] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:44,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:44,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023923085.1_ASM2392308v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:44,945] [INFO] Task started: Blastn
[2024-01-24 12:07:44,945] [INFO] Running command: blastn -query GCF_023923085.1_ASM2392308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4dde3d8-8369-4a90-8c5e-e3791afc1e69/dqc_reference/reference_markers_gtdb.fasta -out GCF_023923085.1_ASM2392308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,662] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,678] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:45,678] [INFO] Target genome list was writen to GCF_023923085.1_ASM2392308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,683] [INFO] Task started: fastANI
[2024-01-24 12:07:45,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgf381416e-3719-4c58-8aa1-fa62e8aab23c/GCF_023923085.1_ASM2392308v1_genomic.fna.gz --refList GCF_023923085.1_ASM2392308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023923085.1_ASM2392308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:51,062] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:51,074] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:51,074] [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	99.9798	843	851	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	83.6664	523	851	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	81.9011	424	851	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	81.8923	449	851	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	81.4493	416	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	79.686	277	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCF_003946605.1	s__Companilactobacillus baiquanensis	79.6628	285	851	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	79.5751	291	851	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	79.2768	244	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.75	99.75	0.93	0.93	2	-
GCF_005404815.1	s__Companilactobacillus huachuanensis	79.1381	258	851	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 12:07:51,076] [INFO] GTDB search result was written to GCF_023923085.1_ASM2392308v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:51,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:51,079] [INFO] DFAST_QC result json was written to GCF_023923085.1_ASM2392308v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:51,080] [INFO] DFAST_QC completed!
[2024-01-24 12:07:51,080] [INFO] Total running time: 0h0m44s