[2024-01-24 15:02:03,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference
[2024-01-24 15:02:06,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,128] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,128] [INFO] Running command: gunzip -c /var/lib/cwl/stgae5a69a2-9b42-4b17-9e64-04aacbf87139/GCF_005405065.1_ASM540506v1_genomic.fna.gz | prodigal -d GCF_005405065.1_ASM540506v1_genomic.fna/cds.fna -a GCF_005405065.1_ASM540506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:13,100] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:13,100] [INFO] Task started: HMMsearch
[2024-01-24 15:02:13,100] [INFO] Running command: hmmsearch --tblout GCF_005405065.1_ASM540506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/reference_markers.hmm GCF_005405065.1_ASM540506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:13,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:13,324] [INFO] Found 6/6 markers.
[2024-01-24 15:02:13,352] [INFO] Query marker FASTA was written to GCF_005405065.1_ASM540506v1_genomic.fna/markers.fasta
[2024-01-24 15:02:13,352] [INFO] Task started: Blastn
[2024-01-24 15:02:13,352] [INFO] Running command: blastn -query GCF_005405065.1_ASM540506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/reference_markers.fasta -out GCF_005405065.1_ASM540506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:15,464] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:15,468] [INFO] Selected 12 target genomes.
[2024-01-24 15:02:15,468] [INFO] Target genome list was writen to GCF_005405065.1_ASM540506v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:15,504] [INFO] Task started: fastANI
[2024-01-24 15:02:15,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgae5a69a2-9b42-4b17-9e64-04aacbf87139/GCF_005405065.1_ASM540506v1_genomic.fna.gz --refList GCF_005405065.1_ASM540506v1_genomic.fna/target_genomes.txt --output GCF_005405065.1_ASM540506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:23,226] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:23,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:23,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:23,252] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:23,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:23,253] [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 nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	100.0	947	947	95	conclusive
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	83.7664	603	947	95	below_threshold
Lactiplantibacillus pingfangensis	strain=382-1	GCA_005404945.1	2559915	2559915	type	True	83.045	567	947	95	below_threshold
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	80.8402	378	947	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	80.4801	415	947	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	80.4584	414	947	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	80.3843	392	947	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	77.2606	62	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:23,263] [INFO] DFAST Taxonomy check result was written to GCF_005405065.1_ASM540506v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:23,264] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:23,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:23,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/checkm_data
[2024-01-24 15:02:23,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:23,298] [INFO] Task started: CheckM
[2024-01-24 15:02:23,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405065.1_ASM540506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405065.1_ASM540506v1_genomic.fna/checkm_input GCF_005405065.1_ASM540506v1_genomic.fna/checkm_result
[2024-01-24 15:02:53,743] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:53,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:53,763] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:53,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:53,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405065.1_ASM540506v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:53,764] [INFO] Task started: Blastn
[2024-01-24 15:02:53,765] [INFO] Running command: blastn -query GCF_005405065.1_ASM540506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7f913b-4c45-49e0-9a16-47f81782b974/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405065.1_ASM540506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:54,672] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:54,675] [INFO] Selected 10 target genomes.
[2024-01-24 15:02:54,676] [INFO] Target genome list was writen to GCF_005405065.1_ASM540506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:54,699] [INFO] Task started: fastANI
[2024-01-24 15:02:54,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgae5a69a2-9b42-4b17-9e64-04aacbf87139/GCF_005405065.1_ASM540506v1_genomic.fna.gz --refList GCF_005405065.1_ASM540506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405065.1_ASM540506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:01,435] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:01,445] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:01,445] [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_005405065.1	s__Lactiplantibacillus nangangensis	100.0	947	947	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	83.7399	606	947	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005404945.1	s__Lactiplantibacillus pingfangensis	83.015	570	947	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	80.7959	380	947	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	80.4727	413	947	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	80.4496	417	947	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	80.4091	390	947	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	80.2421	379	947	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	80.0518	385	947	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 15:03:01,447] [INFO] GTDB search result was written to GCF_005405065.1_ASM540506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:01,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:01,451] [INFO] DFAST_QC result json was written to GCF_005405065.1_ASM540506v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:01,451] [INFO] DFAST_QC completed!
[2024-01-24 15:03:01,452] [INFO] Total running time: 0h0m58s