[2024-01-24 14:56:23,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference
[2024-01-24 14:56:26,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,557] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea8b3e1-0408-40c5-a9ce-0361d5ae0ccc/GCF_000765905.2_ASM76590v2_genomic.fna.gz | prodigal -d GCF_000765905.2_ASM76590v2_genomic.fna/cds.fna -a GCF_000765905.2_ASM76590v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:31,890] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:31,891] [INFO] Task started: HMMsearch
[2024-01-24 14:56:31,891] [INFO] Running command: hmmsearch --tblout GCF_000765905.2_ASM76590v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/reference_markers.hmm GCF_000765905.2_ASM76590v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:32,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:32,249] [INFO] Found 6/6 markers.
[2024-01-24 14:56:32,273] [INFO] Query marker FASTA was written to GCF_000765905.2_ASM76590v2_genomic.fna/markers.fasta
[2024-01-24 14:56:32,274] [INFO] Task started: Blastn
[2024-01-24 14:56:32,274] [INFO] Running command: blastn -query GCF_000765905.2_ASM76590v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/reference_markers.fasta -out GCF_000765905.2_ASM76590v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:36,995] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:36,998] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:36,998] [INFO] Target genome list was writen to GCF_000765905.2_ASM76590v2_genomic.fna/target_genomes.txt
[2024-01-24 14:56:37,039] [INFO] Task started: fastANI
[2024-01-24 14:56:37,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea8b3e1-0408-40c5-a9ce-0361d5ae0ccc/GCF_000765905.2_ASM76590v2_genomic.fna.gz --refList GCF_000765905.2_ASM76590v2_genomic.fna/target_genomes.txt --output GCF_000765905.2_ASM76590v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:42,219] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:42,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:42,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:42,228] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:42,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:42,229] [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 trogontum	strain=ATCC 700114	GCA_000765905.2	50960	50960	type	True	100.0	758	760	95	conclusive
Helicobacter bilis	strain=ATCC 51630	GCA_000765785.2	37372	37372	type	True	82.3988	499	760	95	below_threshold
Helicobacter bilis	strain=ATCC 51630	GCA_000686565.1	37372	37372	type	True	82.336	505	760	95	below_threshold
Helicobacter didelphidarum	strain=MIT 17-337	GCA_003364195.1	2040648	2040648	type	True	77.3823	146	760	95	below_threshold
Helicobacter muridarum	strain=NCTC12714	GCA_900450885.1	216	216	type	True	76.9015	80	760	95	below_threshold
Helicobacter aurati	strain=MIT 97-5075	GCA_003364265.1	137778	137778	type	True	76.4326	72	760	95	below_threshold
Helicobacter saguini	strain=MIT 97-6194	GCA_000762875.2	1548018	1548018	type	True	75.807	72	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:42,230] [INFO] DFAST Taxonomy check result was written to GCF_000765905.2_ASM76590v2_genomic.fna/tc_result.tsv
[2024-01-24 14:56:42,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:42,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:42,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/checkm_data
[2024-01-24 14:56:42,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:42,259] [INFO] Task started: CheckM
[2024-01-24 14:56:42,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000765905.2_ASM76590v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000765905.2_ASM76590v2_genomic.fna/checkm_input GCF_000765905.2_ASM76590v2_genomic.fna/checkm_result
[2024-01-24 14:57:09,714] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:09,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:09,738] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:09,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:09,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000765905.2_ASM76590v2_genomic.fna/markers.fasta)
[2024-01-24 14:57:09,739] [INFO] Task started: Blastn
[2024-01-24 14:57:09,739] [INFO] Running command: blastn -query GCF_000765905.2_ASM76590v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdf4e62-b012-48d2-94c0-bac02bfa5ade/dqc_reference/reference_markers_gtdb.fasta -out GCF_000765905.2_ASM76590v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:10,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:10,557] [INFO] Selected 5 target genomes.
[2024-01-24 14:57:10,557] [INFO] Target genome list was writen to GCF_000765905.2_ASM76590v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:10,563] [INFO] Task started: fastANI
[2024-01-24 14:57:10,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea8b3e1-0408-40c5-a9ce-0361d5ae0ccc/GCF_000765905.2_ASM76590v2_genomic.fna.gz --refList GCF_000765905.2_ASM76590v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000765905.2_ASM76590v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:13,564] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:13,573] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:13,573] [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_000765905.2	s__Helicobacter_A trogontum	100.0	758	760	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.0	97.76	97.01	0.91	0.88	5	conclusive
GCF_000686565.1	s__Helicobacter_A bilis	82.327	506	760	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	82.0105	507	760	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	81.9468	503	760	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	95.8327	99.79	99.65	0.98	0.97	3	-
GCF_001999985.1	s__Helicobacter_A bilis_A	81.767	525	760	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A	96.3516	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:13,575] [INFO] GTDB search result was written to GCF_000765905.2_ASM76590v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:13,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:13,577] [INFO] DFAST_QC result json was written to GCF_000765905.2_ASM76590v2_genomic.fna/dqc_result.json
[2024-01-24 14:57:13,578] [INFO] DFAST_QC completed!
[2024-01-24 14:57:13,578] [INFO] Total running time: 0h0m50s