[2024-01-24 14:28:08,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference
[2024-01-24 14:28:10,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,418] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg751050e8-747e-4775-9296-4f513895dbb2/GCF_005404945.1_ASM540494v1_genomic.fna.gz | prodigal -d GCF_005404945.1_ASM540494v1_genomic.fna/cds.fna -a GCF_005404945.1_ASM540494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:17,313] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:17,314] [INFO] Task started: HMMsearch
[2024-01-24 14:28:17,314] [INFO] Running command: hmmsearch --tblout GCF_005404945.1_ASM540494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/reference_markers.hmm GCF_005404945.1_ASM540494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:17,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:17,629] [INFO] Found 6/6 markers.
[2024-01-24 14:28:17,659] [INFO] Query marker FASTA was written to GCF_005404945.1_ASM540494v1_genomic.fna/markers.fasta
[2024-01-24 14:28:17,659] [INFO] Task started: Blastn
[2024-01-24 14:28:17,659] [INFO] Running command: blastn -query GCF_005404945.1_ASM540494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/reference_markers.fasta -out GCF_005404945.1_ASM540494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:18,381] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:18,385] [INFO] Selected 15 target genomes.
[2024-01-24 14:28:18,385] [INFO] Target genome list was writen to GCF_005404945.1_ASM540494v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:18,427] [INFO] Task started: fastANI
[2024-01-24 14:28:18,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg751050e8-747e-4775-9296-4f513895dbb2/GCF_005404945.1_ASM540494v1_genomic.fna.gz --refList GCF_005404945.1_ASM540494v1_genomic.fna/target_genomes.txt --output GCF_005404945.1_ASM540494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:27,634] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:27,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:27,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:27,645] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:27,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:27,645] [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
Lactiplantibacillus pingfangensis	strain=382-1	GCA_005404945.1	2559915	2559915	type	True	100.0	933	935	95	conclusive
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	84.0387	624	935	95	below_threshold
Lactiplantibacillus nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	83.0397	575	935	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	80.4283	373	935	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	80.2738	382	935	95	below_threshold
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	80.2145	371	935	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	80.2136	396	935	95	below_threshold
Lactiplantibacillus mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	79.9396	362	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:27,649] [INFO] DFAST Taxonomy check result was written to GCF_005404945.1_ASM540494v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:27,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:27,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:27,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/checkm_data
[2024-01-24 14:28:27,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:27,682] [INFO] Task started: CheckM
[2024-01-24 14:28:27,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005404945.1_ASM540494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005404945.1_ASM540494v1_genomic.fna/checkm_input GCF_005404945.1_ASM540494v1_genomic.fna/checkm_result
[2024-01-24 14:28:55,428] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:55,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:55,447] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:55,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:55,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005404945.1_ASM540494v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:55,449] [INFO] Task started: Blastn
[2024-01-24 14:28:55,449] [INFO] Running command: blastn -query GCF_005404945.1_ASM540494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b803fc9-d3a5-4b77-9011-d4f192750b2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005404945.1_ASM540494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:56,293] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:56,296] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:56,296] [INFO] Target genome list was writen to GCF_005404945.1_ASM540494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:56,317] [INFO] Task started: fastANI
[2024-01-24 14:28:56,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg751050e8-747e-4775-9296-4f513895dbb2/GCF_005404945.1_ASM540494v1_genomic.fna.gz --refList GCF_005404945.1_ASM540494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005404945.1_ASM540494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:03,655] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:03,664] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:03,665] [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_005404945.1	s__Lactiplantibacillus pingfangensis	100.0	933	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005405005.1	s__Lactiplantibacillus daoliensis	84.0542	623	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	83.0248	576	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405105.1	s__Lactiplantibacillus dongliensis	80.3809	376	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	80.2797	382	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	80.2145	371	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.2034	396	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_002970935.1	s__Lactiplantibacillus sp002970935	80.1797	373	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970915.1	s__Lactiplantibacillus sp002970915	80.1348	382	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:03,668] [INFO] GTDB search result was written to GCF_005404945.1_ASM540494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:03,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:03,682] [INFO] DFAST_QC result json was written to GCF_005404945.1_ASM540494v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:03,682] [INFO] DFAST_QC completed!
[2024-01-24 14:29:03,682] [INFO] Total running time: 0h0m55s