[2024-01-24 14:12:47,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference
[2024-01-24 14:12:48,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,359] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aa5ff9e-8d1d-4024-9f1a-8a1a87de3c8f/GCF_003364265.1_ASM336426v1_genomic.fna.gz | prodigal -d GCF_003364265.1_ASM336426v1_genomic.fna/cds.fna -a GCF_003364265.1_ASM336426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:52,477] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:52,478] [INFO] Task started: HMMsearch
[2024-01-24 14:12:52,478] [INFO] Running command: hmmsearch --tblout GCF_003364265.1_ASM336426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/reference_markers.hmm GCF_003364265.1_ASM336426v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:52,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:52,734] [INFO] Found 6/6 markers.
[2024-01-24 14:12:52,758] [INFO] Query marker FASTA was written to GCF_003364265.1_ASM336426v1_genomic.fna/markers.fasta
[2024-01-24 14:12:52,758] [INFO] Task started: Blastn
[2024-01-24 14:12:52,758] [INFO] Running command: blastn -query GCF_003364265.1_ASM336426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/reference_markers.fasta -out GCF_003364265.1_ASM336426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:53,330] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:53,333] [INFO] Selected 14 target genomes.
[2024-01-24 14:12:53,334] [INFO] Target genome list was writen to GCF_003364265.1_ASM336426v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:53,367] [INFO] Task started: fastANI
[2024-01-24 14:12:53,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa5ff9e-8d1d-4024-9f1a-8a1a87de3c8f/GCF_003364265.1_ASM336426v1_genomic.fna.gz --refList GCF_003364265.1_ASM336426v1_genomic.fna/target_genomes.txt --output GCF_003364265.1_ASM336426v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:58,034] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:58,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:58,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:58,045] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:58,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:58,045] [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 aurati	strain=MIT 97-5075	GCA_003364265.1	137778	137778	type	True	100.0	636	638	95	conclusive
Helicobacter muridarum	strain=NCTC12714	GCA_900450885.1	216	216	type	True	77.8915	185	638	95	below_threshold
Helicobacter muridarum	strain=ST1	GCA_000765805.2	216	216	type	True	77.7412	185	638	95	below_threshold
Helicobacter didelphidarum	strain=MIT 17-337	GCA_003364195.1	2040648	2040648	type	True	77.0818	85	638	95	below_threshold
Helicobacter trogontum	strain=ATCC 700114	GCA_000765905.2	50960	50960	type	True	76.8828	70	638	95	below_threshold
Helicobacter bilis	strain=ATCC 51630	GCA_000686565.1	37372	37372	type	True	76.8157	77	638	95	below_threshold
Helicobacter bilis	strain=ATCC 51630	GCA_000765785.2	37372	37372	type	True	76.8147	77	638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:58,047] [INFO] DFAST Taxonomy check result was written to GCF_003364265.1_ASM336426v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:58,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:58,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:58,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/checkm_data
[2024-01-24 14:12:58,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:58,072] [INFO] Task started: CheckM
[2024-01-24 14:12:58,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003364265.1_ASM336426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003364265.1_ASM336426v1_genomic.fna/checkm_input GCF_003364265.1_ASM336426v1_genomic.fna/checkm_result
[2024-01-24 14:13:17,406] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:17,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,423] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:17,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:17,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003364265.1_ASM336426v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:17,425] [INFO] Task started: Blastn
[2024-01-24 14:13:17,425] [INFO] Running command: blastn -query GCF_003364265.1_ASM336426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f5fd6b-1e32-4756-b39e-07f57f888096/dqc_reference/reference_markers_gtdb.fasta -out GCF_003364265.1_ASM336426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:18,220] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:18,224] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:18,224] [INFO] Target genome list was writen to GCF_003364265.1_ASM336426v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:18,239] [INFO] Task started: fastANI
[2024-01-24 14:13:18,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa5ff9e-8d1d-4024-9f1a-8a1a87de3c8f/GCF_003364265.1_ASM336426v1_genomic.fna.gz --refList GCF_003364265.1_ASM336426v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003364265.1_ASM336426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:23,015] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:23,033] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:23,033] [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_003364265.1	s__Helicobacter_A aurati	100.0	636	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_000765805.2	s__Helicobacter_A muridarum	77.7413	185	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	99.98	99.97	0.98	0.98	5	-
GCF_003364195.1	s__Helicobacter_A didelphidarum	77.1142	84	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765905.2	s__Helicobacter_A trogontum	76.8828	70	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	97.76	97.01	0.91	0.88	5	-
GCF_001999985.1	s__Helicobacter_A bilis_A	76.8255	76	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.3516	N/A	N/A	N/A	N/A	1	-
GCF_000686565.1	s__Helicobacter_A bilis	76.7872	78	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.5798	99.95	99.91	0.97	0.95	5	-
GCF_900198625.1	s__Helicobacter_A rappini	76.7416	76	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.5798	99.06	97.29	0.97	0.92	4	-
GCF_900198365.1	s__Helicobacter_A bilis_B	76.5306	79	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.8327	99.79	99.65	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:23,036] [INFO] GTDB search result was written to GCF_003364265.1_ASM336426v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:23,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:23,041] [INFO] DFAST_QC result json was written to GCF_003364265.1_ASM336426v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:23,042] [INFO] DFAST_QC completed!
[2024-01-24 14:13:23,042] [INFO] Total running time: 0h0m36s