[2024-01-24 12:36:58,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference
[2024-01-24 12:36:59,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,847] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg573197e2-5321-4e65-8f10-fbf9d6b01f3e/GCF_005405105.1_ASM540510v1_genomic.fna.gz | prodigal -d GCF_005405105.1_ASM540510v1_genomic.fna/cds.fna -a GCF_005405105.1_ASM540510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:06,896] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:06,896] [INFO] Task started: HMMsearch
[2024-01-24 12:37:06,896] [INFO] Running command: hmmsearch --tblout GCF_005405105.1_ASM540510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/reference_markers.hmm GCF_005405105.1_ASM540510v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:07,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:07,242] [INFO] Found 6/6 markers.
[2024-01-24 12:37:07,276] [INFO] Query marker FASTA was written to GCF_005405105.1_ASM540510v1_genomic.fna/markers.fasta
[2024-01-24 12:37:07,276] [INFO] Task started: Blastn
[2024-01-24 12:37:07,276] [INFO] Running command: blastn -query GCF_005405105.1_ASM540510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/reference_markers.fasta -out GCF_005405105.1_ASM540510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:07,908] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:07,912] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:07,912] [INFO] Target genome list was writen to GCF_005405105.1_ASM540510v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:07,930] [INFO] Task started: fastANI
[2024-01-24 12:37:07,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg573197e2-5321-4e65-8f10-fbf9d6b01f3e/GCF_005405105.1_ASM540510v1_genomic.fna.gz --refList GCF_005405105.1_ASM540510v1_genomic.fna/target_genomes.txt --output GCF_005405105.1_ASM540510v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:16,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:16,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:16,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:16,756] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:16,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:16,757] [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 dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	100.0	997	999	95	conclusive
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	91.6874	866	999	95	below_threshold
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	81.0574	477	999	95	below_threshold
Lactiplantibacillus nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	80.5287	382	999	95	below_threshold
Lactiplantibacillus mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	80.5153	451	999	95	below_threshold
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	80.4705	366	999	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	80.4621	375	999	95	below_threshold
Lactiplantibacillus pingfangensis	strain=382-1	GCA_005404945.1	2559915	2559915	type	True	80.3216	381	999	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	78.8747	50	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:16,759] [INFO] DFAST Taxonomy check result was written to GCF_005405105.1_ASM540510v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:16,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:16,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:16,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/checkm_data
[2024-01-24 12:37:16,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:16,797] [INFO] Task started: CheckM
[2024-01-24 12:37:16,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405105.1_ASM540510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405105.1_ASM540510v1_genomic.fna/checkm_input GCF_005405105.1_ASM540510v1_genomic.fna/checkm_result
[2024-01-24 12:37:44,027] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:44,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:44,047] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:44,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:44,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405105.1_ASM540510v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:44,048] [INFO] Task started: Blastn
[2024-01-24 12:37:44,048] [INFO] Running command: blastn -query GCF_005405105.1_ASM540510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg271162c5-0b11-4eac-8e4a-1668bfff4c63/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405105.1_ASM540510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:44,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:44,827] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:44,828] [INFO] Target genome list was writen to GCF_005405105.1_ASM540510v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:44,835] [INFO] Task started: fastANI
[2024-01-24 12:37:44,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg573197e2-5321-4e65-8f10-fbf9d6b01f3e/GCF_005405105.1_ASM540510v1_genomic.fna.gz --refList GCF_005405105.1_ASM540510v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405105.1_ASM540510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:53,382] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,393] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:53,394] [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_005405105.1	s__Lactiplantibacillus dongliensis	100.0	997	999	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_005405125.1	s__Lactiplantibacillus songbeiensis	91.6874	866	999	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	81.0298	479	999	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	80.5582	379	999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405385.1	s__Lactiplantibacillus mudanjiangensis	80.5071	452	999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.38	99.14	0.94	0.91	5	-
GCF_005405005.1	s__Lactiplantibacillus daoliensis	80.4865	365	999	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	80.4621	375	999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005404945.1	s__Lactiplantibacillus pingfangensis	80.3216	381	999	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	80.1192	349	999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970935.1	s__Lactiplantibacillus sp002970935	80.076	350	999	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 12:37:53,395] [INFO] GTDB search result was written to GCF_005405105.1_ASM540510v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:53,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:53,398] [INFO] DFAST_QC result json was written to GCF_005405105.1_ASM540510v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:53,399] [INFO] DFAST_QC completed!
[2024-01-24 12:37:53,399] [INFO] Total running time: 0h0m55s