[2024-01-24 12:00:36,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference
[2024-01-24 12:00:39,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,378] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bcb3dc3-be0f-4e2c-aca8-11a615b225af/GCF_019061205.1_ASM1906120v1_genomic.fna.gz | prodigal -d GCF_019061205.1_ASM1906120v1_genomic.fna/cds.fna -a GCF_019061205.1_ASM1906120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:42,518] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:42,519] [INFO] Task started: HMMsearch
[2024-01-24 12:00:42,519] [INFO] Running command: hmmsearch --tblout GCF_019061205.1_ASM1906120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/reference_markers.hmm GCF_019061205.1_ASM1906120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:42,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:42,728] [INFO] Found 6/6 markers.
[2024-01-24 12:00:42,745] [INFO] Query marker FASTA was written to GCF_019061205.1_ASM1906120v1_genomic.fna/markers.fasta
[2024-01-24 12:00:42,746] [INFO] Task started: Blastn
[2024-01-24 12:00:42,746] [INFO] Running command: blastn -query GCF_019061205.1_ASM1906120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/reference_markers.fasta -out GCF_019061205.1_ASM1906120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,177] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,181] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:45,182] [INFO] Target genome list was writen to GCF_019061205.1_ASM1906120v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:45,241] [INFO] Task started: fastANI
[2024-01-24 12:00:45,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bcb3dc3-be0f-4e2c-aca8-11a615b225af/GCF_019061205.1_ASM1906120v1_genomic.fna.gz --refList GCF_019061205.1_ASM1906120v1_genomic.fna/target_genomes.txt --output GCF_019061205.1_ASM1906120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:48,199] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:48,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:48,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:48,211] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:48,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:48,211] [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
Apilactobacillus waqarii	strain=HBW1	GCA_019061205.1	2851006	2851006	type	True	100.0	485	486	95	conclusive
Apilactobacillus nanyangensis	strain=HN36-1	GCA_016861915.1	2799579	2799579	type	True	93.7762	408	486	95	below_threshold
Apilactobacillus kunkeei	strain=YH-15	GCA_001281265.1	148814	148814	suspected-type	True	93.5446	455	486	95	below_threshold
Apilactobacillus kunkeei	strain=DSM 12361	GCA_001433825.1	148814	148814	suspected-type	True	93.4905	455	486	95	below_threshold
Apilactobacillus zhangqiuensis	strain=F502-1	GCA_019656215.1	2841031	2841031	type	True	92.1741	448	486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:48,214] [INFO] DFAST Taxonomy check result was written to GCF_019061205.1_ASM1906120v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:48,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:48,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:48,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/checkm_data
[2024-01-24 12:00:48,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:48,237] [INFO] Task started: CheckM
[2024-01-24 12:00:48,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019061205.1_ASM1906120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019061205.1_ASM1906120v1_genomic.fna/checkm_input GCF_019061205.1_ASM1906120v1_genomic.fna/checkm_result
[2024-01-24 12:01:07,717] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:07,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:07,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:07,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:07,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019061205.1_ASM1906120v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:07,742] [INFO] Task started: Blastn
[2024-01-24 12:01:07,742] [INFO] Running command: blastn -query GCF_019061205.1_ASM1906120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6062cb27-7a4a-425f-9d4d-e9dcf10869e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_019061205.1_ASM1906120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:08,484] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:08,489] [INFO] Selected 6 target genomes.
[2024-01-24 12:01:08,489] [INFO] Target genome list was writen to GCF_019061205.1_ASM1906120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:08,495] [INFO] Task started: fastANI
[2024-01-24 12:01:08,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bcb3dc3-be0f-4e2c-aca8-11a615b225af/GCF_019061205.1_ASM1906120v1_genomic.fna.gz --refList GCF_019061205.1_ASM1906120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019061205.1_ASM1906120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:10,702] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:10,708] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:10,708] [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_001949975.2	s__Apilactobacillus kunkeei_A	97.8147	460	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	96.15	95.05	0.91	0.88	13	conclusive
GCF_001308195.1	s__Apilactobacillus kunkeei_C	94.6754	442	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	95.16	95.16	0.91	0.91	2	-
GCF_005930915.1	s__Apilactobacillus kunkeei_D	93.5611	420	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.78	97.92	0.96	0.94	5	-
GCF_001281265.1	s__Apilactobacillus kunkeei	93.5446	455	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	97.63	95.32	0.94	0.90	8	-
GCF_001308205.1	s__Apilactobacillus kunkeei_B	92.3512	439	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	91.589	426	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:10,710] [INFO] GTDB search result was written to GCF_019061205.1_ASM1906120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:10,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:10,715] [INFO] DFAST_QC result json was written to GCF_019061205.1_ASM1906120v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:10,715] [INFO] DFAST_QC completed!
[2024-01-24 12:01:10,715] [INFO] Total running time: 0h0m34s