[2024-01-24 13:18:25,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:25,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:25,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference
[2024-01-24 13:18:26,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:26,736] [INFO] Task started: Prodigal
[2024-01-24 13:18:26,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f3f8a32-3793-45fb-9625-bf276281fc39/GCF_009764345.1_ASM976434v1_genomic.fna.gz | prodigal -d GCF_009764345.1_ASM976434v1_genomic.fna/cds.fna -a GCF_009764345.1_ASM976434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:31,581] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:31,581] [INFO] Task started: HMMsearch
[2024-01-24 13:18:31,581] [INFO] Running command: hmmsearch --tblout GCF_009764345.1_ASM976434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/reference_markers.hmm GCF_009764345.1_ASM976434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:31,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:31,772] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4f3f8a32-3793-45fb-9625-bf276281fc39/GCF_009764345.1_ASM976434v1_genomic.fna.gz]
[2024-01-24 13:18:31,803] [INFO] Query marker FASTA was written to GCF_009764345.1_ASM976434v1_genomic.fna/markers.fasta
[2024-01-24 13:18:31,803] [INFO] Task started: Blastn
[2024-01-24 13:18:31,803] [INFO] Running command: blastn -query GCF_009764345.1_ASM976434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/reference_markers.fasta -out GCF_009764345.1_ASM976434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:32,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:32,362] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:32,362] [INFO] Target genome list was writen to GCF_009764345.1_ASM976434v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:32,367] [INFO] Task started: fastANI
[2024-01-24 13:18:32,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f8a32-3793-45fb-9625-bf276281fc39/GCF_009764345.1_ASM976434v1_genomic.fna.gz --refList GCF_009764345.1_ASM976434v1_genomic.fna/target_genomes.txt --output GCF_009764345.1_ASM976434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:37,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:37,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:37,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:37,981] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:37,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:37,982] [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 paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	100.0	811	827	95	conclusive
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_001434985.1	83526	83526	type	True	99.965	743	827	95	conclusive
Companilactobacillus paralimentarius	strain=JCM 10415	GCA_000615725.1	83526	83526	type	True	99.8756	706	827	95	conclusive
Companilactobacillus kimchii	strain=DSM 13961	GCA_001435445.1	2801452	2801452	type	True	91.9161	689	827	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	91.8264	697	827	95	below_threshold
Companilactobacillus bobalius	strain=DSM 19674	GCA_001434855.1	2801451	2801451	type	True	91.4136	717	827	95	below_threshold
Companilactobacillus bobalius	strain=203	GCA_009764355.1	2801451	2801451	type	True	91.2888	730	827	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.4436	253	827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:37,983] [INFO] DFAST Taxonomy check result was written to GCF_009764345.1_ASM976434v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:37,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:37,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:37,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/checkm_data
[2024-01-24 13:18:37,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:38,028] [INFO] Task started: CheckM
[2024-01-24 13:18:38,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009764345.1_ASM976434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009764345.1_ASM976434v1_genomic.fna/checkm_input GCF_009764345.1_ASM976434v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,205] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009764345.1_ASM976434v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,206] [INFO] Task started: Blastn
[2024-01-24 13:19:00,206] [INFO] Running command: blastn -query GCF_009764345.1_ASM976434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg055610df-1170-4cce-b5a8-b81b394bd92f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009764345.1_ASM976434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,963] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:00,963] [INFO] Target genome list was writen to GCF_009764345.1_ASM976434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:00,971] [INFO] Task started: fastANI
[2024-01-24 13:19:00,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f8a32-3793-45fb-9625-bf276281fc39/GCF_009764345.1_ASM976434v1_genomic.fna.gz --refList GCF_009764345.1_ASM976434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009764345.1_ASM976434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:06,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:06,748] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:06,748] [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_001434985.1	s__Companilactobacillus paralimentarius	99.965	743	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.97	99.96	0.99	0.99	4	conclusive
GCF_001435445.1	s__Companilactobacillus kimchii	91.9161	689	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	-
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	91.3363	729	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCA_019116025.1	s__Companilactobacillus pullicola	86.5031	617	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849895.1	s__Companilactobacillus alimentarius	83.0579	509	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	82.5385	468	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872255.1	s__Companilactobacillus nuruki	81.7287	406	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	81.6375	409	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435815.1	s__Companilactobacillus nantensis	81.4647	425	827	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,749] [INFO] GTDB search result was written to GCF_009764345.1_ASM976434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:06,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:06,753] [INFO] DFAST_QC result json was written to GCF_009764345.1_ASM976434v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:06,753] [INFO] DFAST_QC completed!
[2024-01-24 13:19:06,753] [INFO] Total running time: 0h0m41s