[2024-01-24 11:58:20,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,238] [INFO] DQC Reference Directory: /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference
[2024-01-24 11:58:21,473] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,474] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,475] [INFO] Running command: gunzip -c /var/lib/cwl/stgd154dce0-c7a4-4d74-828f-d8d170b93d89/GCF_001434985.1_ASM143498v1_genomic.fna.gz | prodigal -d GCF_001434985.1_ASM143498v1_genomic.fna/cds.fna -a GCF_001434985.1_ASM143498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:26,145] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:26,145] [INFO] Task started: HMMsearch
[2024-01-24 11:58:26,145] [INFO] Running command: hmmsearch --tblout GCF_001434985.1_ASM143498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/reference_markers.hmm GCF_001434985.1_ASM143498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:26,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:26,376] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd154dce0-c7a4-4d74-828f-d8d170b93d89/GCF_001434985.1_ASM143498v1_genomic.fna.gz]
[2024-01-24 11:58:26,403] [INFO] Query marker FASTA was written to GCF_001434985.1_ASM143498v1_genomic.fna/markers.fasta
[2024-01-24 11:58:26,403] [INFO] Task started: Blastn
[2024-01-24 11:58:26,403] [INFO] Running command: blastn -query GCF_001434985.1_ASM143498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/reference_markers.fasta -out GCF_001434985.1_ASM143498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:26,974] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:26,978] [INFO] Selected 10 target genomes.
[2024-01-24 11:58:26,979] [INFO] Target genome list was writen to GCF_001434985.1_ASM143498v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:27,015] [INFO] Task started: fastANI
[2024-01-24 11:58:27,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgd154dce0-c7a4-4d74-828f-d8d170b93d89/GCF_001434985.1_ASM143498v1_genomic.fna.gz --refList GCF_001434985.1_ASM143498v1_genomic.fna/target_genomes.txt --output GCF_001434985.1_ASM143498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:32,494] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:32,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:32,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:32,507] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:58:32,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:58:32,507] [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_001434985.1	83526	83526	type	True	100.0	770	781	95	conclusive
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	99.9665	778	781	95	conclusive
Companilactobacillus paralimentarius	strain=JCM 10415	GCA_000615725.1	83526	83526	type	True	99.905	698	781	95	conclusive
Companilactobacillus kimchii	strain=DSM 13961	GCA_001435445.1	2801452	2801452	type	True	91.8837	685	781	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	91.8607	688	781	95	below_threshold
Companilactobacillus bobalius	strain=DSM 19674	GCA_001434855.1	2801451	2801451	type	True	91.4959	707	781	95	below_threshold
Companilactobacillus bobalius	strain=203	GCA_009764355.1	2801451	2801451	type	True	91.4415	720	781	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.1064	247	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:32,509] [INFO] DFAST Taxonomy check result was written to GCF_001434985.1_ASM143498v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:32,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:32,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:32,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/checkm_data
[2024-01-24 11:58:32,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:32,536] [INFO] Task started: CheckM
[2024-01-24 11:58:32,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434985.1_ASM143498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434985.1_ASM143498v1_genomic.fna/checkm_input GCF_001434985.1_ASM143498v1_genomic.fna/checkm_result
[2024-01-24 11:58:53,730] [INFO] Task succeeded: CheckM
[2024-01-24 11:58:53,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:58:53,753] [INFO] ===== Completeness check finished =====
[2024-01-24 11:58:53,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:58:53,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434985.1_ASM143498v1_genomic.fna/markers.fasta)
[2024-01-24 11:58:53,754] [INFO] Task started: Blastn
[2024-01-24 11:58:53,755] [INFO] Running command: blastn -query GCF_001434985.1_ASM143498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc27d947a-1e6c-452b-9be1-6bfa44fd6c52/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434985.1_ASM143498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:54,483] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:54,487] [INFO] Selected 9 target genomes.
[2024-01-24 11:58:54,487] [INFO] Target genome list was writen to GCF_001434985.1_ASM143498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:58:54,497] [INFO] Task started: fastANI
[2024-01-24 11:58:54,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgd154dce0-c7a4-4d74-828f-d8d170b93d89/GCF_001434985.1_ASM143498v1_genomic.fna.gz --refList GCF_001434985.1_ASM143498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434985.1_ASM143498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:58:59,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:59,874] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:58:59,875] [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	100.0	770	781	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	91.8837	685	781	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	91.4199	722	781	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	86.6092	621	781	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	82.8363	502	781	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	82.597	451	781	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	81.6844	389	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435815.1	s__Companilactobacillus nantensis	81.5925	412	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	81.4961	403	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:58:59,876] [INFO] GTDB search result was written to GCF_001434985.1_ASM143498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:58:59,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:58:59,879] [INFO] DFAST_QC result json was written to GCF_001434985.1_ASM143498v1_genomic.fna/dqc_result.json
[2024-01-24 11:58:59,879] [INFO] DFAST_QC completed!
[2024-01-24 11:58:59,880] [INFO] Total running time: 0h0m40s