[2023-06-05 00:30:31,546] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:31,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:31,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference
[2023-06-05 00:30:33,109] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:33,111] [INFO] Task started: Prodigal
[2023-06-05 00:30:33,111] [INFO] Running command: gunzip -c /var/lib/cwl/stgce40e44c-22a0-4fc4-8e17-e8e12128e46a/GCA_934478095.1_ERR7738161_bin.20_genomic.fna.gz | prodigal -d GCA_934478095.1_ERR7738161_bin.20_genomic.fna/cds.fna -a GCA_934478095.1_ERR7738161_bin.20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:36,668] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:36,668] [INFO] Task started: HMMsearch
[2023-06-05 00:30:36,668] [INFO] Running command: hmmsearch --tblout GCA_934478095.1_ERR7738161_bin.20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/reference_markers.hmm GCA_934478095.1_ERR7738161_bin.20_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:36,890] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:36,892] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgce40e44c-22a0-4fc4-8e17-e8e12128e46a/GCA_934478095.1_ERR7738161_bin.20_genomic.fna.gz]
[2023-06-05 00:30:36,912] [INFO] Query marker FASTA was written to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/markers.fasta
[2023-06-05 00:30:36,912] [INFO] Task started: Blastn
[2023-06-05 00:30:36,913] [INFO] Running command: blastn -query GCA_934478095.1_ERR7738161_bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/reference_markers.fasta -out GCA_934478095.1_ERR7738161_bin.20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:37,448] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:37,452] [INFO] Selected 12 target genomes.
[2023-06-05 00:30:37,452] [INFO] Target genome list was writen to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/target_genomes.txt
[2023-06-05 00:30:37,517] [INFO] Task started: fastANI
[2023-06-05 00:30:37,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgce40e44c-22a0-4fc4-8e17-e8e12128e46a/GCA_934478095.1_ERR7738161_bin.20_genomic.fna.gz --refList GCA_934478095.1_ERR7738161_bin.20_genomic.fna/target_genomes.txt --output GCA_934478095.1_ERR7738161_bin.20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:42,565] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:42,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:42,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:42,574] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2023-06-05 00:30:42,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 00:30:42,574] [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
Lacticaseibacillus pantheris	strain=DSM 15945	GCA_001435155.1	171523	171523	type	True	98.7888	232	239	95	conclusive
Lacticaseibacillus pantheris	strain=JCM 12539	GCA_001311175.1	171523	171523	type	True	98.6818	233	239	95	conclusive
Lacticaseibacillus pantheris	strain=NBRC 106106	GCA_001591865.1	171523	171523	type	True	98.5846	231	239	95	conclusive
Lacticaseibacillus thailandensis	strain=DSM 22698	GCA_001436135.1	381741	381741	type	True	80.8456	131	239	95	below_threshold
Lacticaseibacillus thailandensis	strain=JCM 13996	GCA_001312865.1	381741	381741	type	True	80.8258	131	239	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:30:42,576] [INFO] DFAST Taxonomy check result was written to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/tc_result.tsv
[2023-06-05 00:30:42,577] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:42,577] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:42,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/checkm_data
[2023-06-05 00:30:42,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:42,598] [INFO] Task started: CheckM
[2023-06-05 00:30:42,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934478095.1_ERR7738161_bin.20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934478095.1_ERR7738161_bin.20_genomic.fna/checkm_input GCA_934478095.1_ERR7738161_bin.20_genomic.fna/checkm_result
[2023-06-05 00:31:00,936] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:00,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:31:00,956] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:00,957] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:00,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934478095.1_ERR7738161_bin.20_genomic.fna/markers.fasta)
[2023-06-05 00:31:00,958] [INFO] Task started: Blastn
[2023-06-05 00:31:00,958] [INFO] Running command: blastn -query GCA_934478095.1_ERR7738161_bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0387cc2-ab1a-4943-b550-f621fa3f9316/dqc_reference/reference_markers_gtdb.fasta -out GCA_934478095.1_ERR7738161_bin.20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:01,415] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:01,419] [INFO] Selected 12 target genomes.
[2023-06-05 00:31:01,420] [INFO] Target genome list was writen to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:01,563] [INFO] Task started: fastANI
[2023-06-05 00:31:01,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgce40e44c-22a0-4fc4-8e17-e8e12128e46a/GCA_934478095.1_ERR7738161_bin.20_genomic.fna.gz --refList GCA_934478095.1_ERR7738161_bin.20_genomic.fna/target_genomes_gtdb.txt --output GCA_934478095.1_ERR7738161_bin.20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:07,524] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:07,530] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:31:07,531] [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_001311175.1	s__Lacticaseibacillus pantheris	98.6818	233	239	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	0.99	0.98	3	conclusive
GCF_001312865.1	s__Lacticaseibacillus thailandensis	80.8258	131	239	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:31:07,536] [INFO] GTDB search result was written to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:07,536] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:07,540] [INFO] DFAST_QC result json was written to GCA_934478095.1_ERR7738161_bin.20_genomic.fna/dqc_result.json
[2023-06-05 00:31:07,540] [INFO] DFAST_QC completed!
[2023-06-05 00:31:07,541] [INFO] Total running time: 0h0m36s