[2024-01-24 13:40:55,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference
[2024-01-24 13:40:56,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,748] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg7de34a0c-680c-4ba2-987f-bdeac8878e3b/GCF_003050665.1_ASM305066v1_genomic.fna.gz | prodigal -d GCF_003050665.1_ASM305066v1_genomic.fna/cds.fna -a GCF_003050665.1_ASM305066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,201] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,201] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,201] [INFO] Running command: hmmsearch --tblout GCF_003050665.1_ASM305066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/reference_markers.hmm GCF_003050665.1_ASM305066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,439] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,460] [INFO] Query marker FASTA was written to GCF_003050665.1_ASM305066v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,461] [INFO] Task started: Blastn
[2024-01-24 13:41:00,461] [INFO] Running command: blastn -query GCF_003050665.1_ASM305066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/reference_markers.fasta -out GCF_003050665.1_ASM305066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,034] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,037] [INFO] Selected 6 target genomes.
[2024-01-24 13:41:01,038] [INFO] Target genome list was writen to GCF_003050665.1_ASM305066v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,043] [INFO] Task started: fastANI
[2024-01-24 13:41:01,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de34a0c-680c-4ba2-987f-bdeac8878e3b/GCF_003050665.1_ASM305066v1_genomic.fna.gz --refList GCF_003050665.1_ASM305066v1_genomic.fna/target_genomes.txt --output GCF_003050665.1_ASM305066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:03,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:03,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:03,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:03,714] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:41:03,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:03,715] [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
Helicobacter pylori	strain=FDAARGOS_298	GCA_003050665.1	210	210	type	True	100.0	559	560	95	conclusive
Helicobacter pylori	strain=NCTC 11637	GCA_900478295.1	210	210	type	True	99.9957	559	560	95	conclusive
Helicobacter pylori	strain=ATCC 43504	GCA_004295525.1	210	210	type	True	99.9939	560	560	95	conclusive
Helicobacter pylori	strain=CCUG 17874	GCA_000258845.1	210	210	type	True	95.6056	435	560	95	conclusive
Helicobacter pylori	strain=JCM 12093	GCA_014654435.1	210	210	type	True	95.4795	464	560	95	conclusive
Helicobacter acinonychis	strain=NCTC12686	GCA_900461455.1	212	212	type	True	89.5586	458	560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:03,716] [INFO] DFAST Taxonomy check result was written to GCF_003050665.1_ASM305066v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:03,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:03,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:03,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/checkm_data
[2024-01-24 13:41:03,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:03,752] [INFO] Task started: CheckM
[2024-01-24 13:41:03,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003050665.1_ASM305066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003050665.1_ASM305066v1_genomic.fna/checkm_input GCF_003050665.1_ASM305066v1_genomic.fna/checkm_result
[2024-01-24 13:41:20,540] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:20,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:20,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:20,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:20,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003050665.1_ASM305066v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:20,571] [INFO] Task started: Blastn
[2024-01-24 13:41:20,571] [INFO] Running command: blastn -query GCF_003050665.1_ASM305066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc3d2ed-03cd-479b-9653-e6c99c79fd3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003050665.1_ASM305066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:21,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:21,405] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:21,406] [INFO] Target genome list was writen to GCF_003050665.1_ASM305066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:21,412] [INFO] Task started: fastANI
[2024-01-24 13:41:21,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de34a0c-680c-4ba2-987f-bdeac8878e3b/GCF_003050665.1_ASM305066v1_genomic.fna.gz --refList GCF_003050665.1_ASM305066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003050665.1_ASM305066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:25,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:25,179] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:25,179] [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_900478295.1	s__Helicobacter pylori	99.9957	560	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1033	95.74	95.20	0.96	0.89	759	conclusive
GCF_009689985.1	s__Helicobacter pylori_CG	95.1643	496	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.2184	95.73	95.28	0.94	0.91	8	-
GCF_000448485.1	s__Helicobacter pylori_CI	95.0273	392	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0968	95.60	95.24	0.92	0.84	283	-
GCF_003637665.1	s__Helicobacter pylori_CK	95.0189	506	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0255	95.54	95.27	0.95	0.93	16	-
GCF_000476275.1	s__Helicobacter pylori_CL	94.9603	480	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0096	99.99	99.99	0.99	0.99	2	-
GCF_000277405.1	s__Helicobacter pylori_C	94.9316	515	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.2184	96.43	95.23	0.96	0.89	435	-
GCF_003636935.1	s__Helicobacter pylori_CH	94.8282	499	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003637685.1	s__Helicobacter pylori_CJ	94.8213	500	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1579	95.67	95.36	0.94	0.91	66	-
GCF_001653475.1	s__Helicobacter pylori_CM	94.4952	495	560	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1561	95.99	95.99	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,180] [INFO] GTDB search result was written to GCF_003050665.1_ASM305066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:25,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:25,183] [INFO] DFAST_QC result json was written to GCF_003050665.1_ASM305066v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:25,184] [INFO] DFAST_QC completed!
[2024-01-24 13:41:25,184] [INFO] Total running time: 0h0m30s