[2024-01-24 12:22:38,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:38,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:38,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference
[2024-01-24 12:22:39,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,395] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg66da8496-8243-469f-8f9b-3f5f2be94b32/GCF_005404815.1_ASM540481v1_genomic.fna.gz | prodigal -d GCF_005404815.1_ASM540481v1_genomic.fna/cds.fna -a GCF_005404815.1_ASM540481v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:45,566] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:45,566] [INFO] Task started: HMMsearch
[2024-01-24 12:22:45,566] [INFO] Running command: hmmsearch --tblout GCF_005404815.1_ASM540481v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/reference_markers.hmm GCF_005404815.1_ASM540481v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:45,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:45,828] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg66da8496-8243-469f-8f9b-3f5f2be94b32/GCF_005404815.1_ASM540481v1_genomic.fna.gz]
[2024-01-24 12:22:45,860] [INFO] Query marker FASTA was written to GCF_005404815.1_ASM540481v1_genomic.fna/markers.fasta
[2024-01-24 12:22:45,860] [INFO] Task started: Blastn
[2024-01-24 12:22:45,861] [INFO] Running command: blastn -query GCF_005404815.1_ASM540481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/reference_markers.fasta -out GCF_005404815.1_ASM540481v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:46,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:46,491] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:46,491] [INFO] Target genome list was writen to GCF_005404815.1_ASM540481v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:46,497] [INFO] Task started: fastANI
[2024-01-24 12:22:46,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg66da8496-8243-469f-8f9b-3f5f2be94b32/GCF_005404815.1_ASM540481v1_genomic.fna.gz --refList GCF_005404815.1_ASM540481v1_genomic.fna/target_genomes.txt --output GCF_005404815.1_ASM540481v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:00,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:00,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:00,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:00,970] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:00,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:00,971] [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 huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	100.0	974	979	95	conclusive
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	87.297	748	979	95	below_threshold
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	87.2583	758	979	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	84.3713	654	979	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	83.7127	629	979	95	below_threshold
Companilactobacillus musae	strain=NBRC 112868	GCA_003967595.1	1903258	1903258	type	True	82.5031	472	979	95	below_threshold
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	82.499	479	979	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.2092	423	979	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.2054	402	979	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:00,973] [INFO] DFAST Taxonomy check result was written to GCF_005404815.1_ASM540481v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:00,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:00,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:00,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/checkm_data
[2024-01-24 12:23:00,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:01,009] [INFO] Task started: CheckM
[2024-01-24 12:23:01,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005404815.1_ASM540481v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005404815.1_ASM540481v1_genomic.fna/checkm_input GCF_005404815.1_ASM540481v1_genomic.fna/checkm_result
[2024-01-24 12:23:26,255] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:26,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:26,277] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:26,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:26,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005404815.1_ASM540481v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:26,278] [INFO] Task started: Blastn
[2024-01-24 12:23:26,278] [INFO] Running command: blastn -query GCF_005404815.1_ASM540481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e049a2d-7162-48dc-bfe6-d0cd65041bdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_005404815.1_ASM540481v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:27,017] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:27,021] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:27,021] [INFO] Target genome list was writen to GCF_005404815.1_ASM540481v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:27,028] [INFO] Task started: fastANI
[2024-01-24 12:23:27,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg66da8496-8243-469f-8f9b-3f5f2be94b32/GCF_005404815.1_ASM540481v1_genomic.fna.gz --refList GCF_005404815.1_ASM540481v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005404815.1_ASM540481v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:38,196] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:38,210] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:38,211] [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_005404815.1	s__Companilactobacillus huachuanensis	100.0	974	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	87.2275	759	979	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	84.398	652	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003606365.2	s__Companilactobacillus zhachilii	83.7306	628	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_003967595.1	s__Companilactobacillus musae	82.5197	472	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001438805.1	s__Companilactobacillus kimchiensis	82.1367	510	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434275.1	s__Companilactobacillus mindensis	81.7782	445	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002872255.1	s__Companilactobacillus nuruki	81.7333	457	979	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:38,214] [INFO] GTDB search result was written to GCF_005404815.1_ASM540481v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:38,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:38,218] [INFO] DFAST_QC result json was written to GCF_005404815.1_ASM540481v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:38,219] [INFO] DFAST_QC completed!
[2024-01-24 12:23:38,219] [INFO] Total running time: 0h1m0s