[2024-01-24 13:42:56,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:56,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:56,976] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference
[2024-01-24 13:42:58,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,240] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg19b0f4b3-480c-480e-a00b-29450bdf2c9e/GCF_008693005.1_ASM869300v1_genomic.fna.gz | prodigal -d GCF_008693005.1_ASM869300v1_genomic.fna/cds.fna -a GCF_008693005.1_ASM869300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:02,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:02,966] [INFO] Task started: HMMsearch
[2024-01-24 13:43:02,966] [INFO] Running command: hmmsearch --tblout GCF_008693005.1_ASM869300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/reference_markers.hmm GCF_008693005.1_ASM869300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:03,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:03,230] [INFO] Found 6/6 markers.
[2024-01-24 13:43:03,254] [INFO] Query marker FASTA was written to GCF_008693005.1_ASM869300v1_genomic.fna/markers.fasta
[2024-01-24 13:43:03,255] [INFO] Task started: Blastn
[2024-01-24 13:43:03,255] [INFO] Running command: blastn -query GCF_008693005.1_ASM869300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/reference_markers.fasta -out GCF_008693005.1_ASM869300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:03,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:03,846] [INFO] Selected 12 target genomes.
[2024-01-24 13:43:03,846] [INFO] Target genome list was writen to GCF_008693005.1_ASM869300v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:03,887] [INFO] Task started: fastANI
[2024-01-24 13:43:03,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b0f4b3-480c-480e-a00b-29450bdf2c9e/GCF_008693005.1_ASM869300v1_genomic.fna.gz --refList GCF_008693005.1_ASM869300v1_genomic.fna/target_genomes.txt --output GCF_008693005.1_ASM869300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:08,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:08,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:08,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:08,469] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:43:08,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:08,469] [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 canis	strain=CCUG 32756T	GCA_008693005.1	29419	29419	type	True	100.0	626	629	95	conclusive
Helicobacter canis	strain=CCUG 32756	GCA_017979455.1	29419	29419	type	True	99.9682	578	629	95	conclusive
Helicobacter cinaedi	strain=CCUG 18818	GCA_000155475.1	213	213	type	True	82.2828	115	629	95	below_threshold
Helicobacter cinaedi	strain=CCUG 18818	GCA_003215615.1	213	213	type	True	82.1346	114	629	95	below_threshold
Helicobacter cinaedi	strain=DSM 5359	GCA_017979495.1	213	213	type	True	81.9015	120	629	95	below_threshold
Helicobacter winghamensis	strain=ATCC BAA-430	GCA_000158455.1	157268	157268	type	True	79.7286	54	629	95	below_threshold
Helicobacter fennelliae	strain=DSM 7491	GCA_017979365.1	215	215	suspected-type	True	77.6525	98	629	95	below_threshold
Helicobacter macacae	strain=MIT 99-5501	GCA_000507845.1	398626	398626	type	True	76.7719	129	629	95	below_threshold
Helicobacter marmotae	strain=MIT 98-6070	GCA_003364255.1	152490	152490	type	True	76.7397	55	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:08,471] [INFO] DFAST Taxonomy check result was written to GCF_008693005.1_ASM869300v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:08,472] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:08,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:08,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/checkm_data
[2024-01-24 13:43:08,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:08,498] [INFO] Task started: CheckM
[2024-01-24 13:43:08,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008693005.1_ASM869300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008693005.1_ASM869300v1_genomic.fna/checkm_input GCF_008693005.1_ASM869300v1_genomic.fna/checkm_result
[2024-01-24 13:43:28,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:28,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:28,970] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:28,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:28,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008693005.1_ASM869300v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:28,971] [INFO] Task started: Blastn
[2024-01-24 13:43:28,971] [INFO] Running command: blastn -query GCF_008693005.1_ASM869300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bca356-cc32-43b9-9f2e-10a46f41df3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008693005.1_ASM869300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:29,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:29,770] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:29,770] [INFO] Target genome list was writen to GCF_008693005.1_ASM869300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:29,791] [INFO] Task started: fastANI
[2024-01-24 13:43:29,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b0f4b3-480c-480e-a00b-29450bdf2c9e/GCF_008693005.1_ASM869300v1_genomic.fna.gz --refList GCF_008693005.1_ASM869300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008693005.1_ASM869300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:34,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:34,031] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:34,031] [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_008693005.1	s__Helicobacter_B canis	100.0	626	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	97.15	95.72	0.95	0.93	4	conclusive
GCA_017502485.1	s__Helicobacter_B sp017502485	88.7399	508	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451095.1	s__Helicobacter_B canis_B	87.1095	547	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155475.1	s__Helicobacter_C cinaedi	82.146	116	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.33	98.84	0.97	0.91	38	-
GCF_000158455.1	s__Helicobacter_D winghamensis	79.7286	54	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.73	99.12	0.98	0.96	8	-
GCF_017979365.1	s__Helicobacter_B fennelliae	77.6812	97	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.60	99.16	0.90	0.87	5	-
GCF_001854545.1	s__Helicobacter_B sp001854545	77.254	156	629	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.98	99.96	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:34,033] [INFO] GTDB search result was written to GCF_008693005.1_ASM869300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:34,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:34,036] [INFO] DFAST_QC result json was written to GCF_008693005.1_ASM869300v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:34,036] [INFO] DFAST_QC completed!
[2024-01-24 13:43:34,036] [INFO] Total running time: 0h0m37s