[2024-01-25 17:37:20,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:20,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:20,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference
[2024-01-25 17:37:21,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:21,916] [INFO] Task started: Prodigal
[2024-01-25 17:37:21,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ce50194-1374-494c-87c0-c8884c63fc58/GCF_017979375.1_ASM1797937v1_genomic.fna.gz | prodigal -d GCF_017979375.1_ASM1797937v1_genomic.fna/cds.fna -a GCF_017979375.1_ASM1797937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:24,626] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:24,627] [INFO] Task started: HMMsearch
[2024-01-25 17:37:24,627] [INFO] Running command: hmmsearch --tblout GCF_017979375.1_ASM1797937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/reference_markers.hmm GCF_017979375.1_ASM1797937v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:24,891] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:24,892] [INFO] Found 6/6 markers.
[2024-01-25 17:37:24,921] [INFO] Query marker FASTA was written to GCF_017979375.1_ASM1797937v1_genomic.fna/markers.fasta
[2024-01-25 17:37:24,922] [INFO] Task started: Blastn
[2024-01-25 17:37:24,922] [INFO] Running command: blastn -query GCF_017979375.1_ASM1797937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/reference_markers.fasta -out GCF_017979375.1_ASM1797937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:25,434] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:25,438] [INFO] Selected 10 target genomes.
[2024-01-25 17:37:25,438] [INFO] Target genome list was writen to GCF_017979375.1_ASM1797937v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:25,442] [INFO] Task started: fastANI
[2024-01-25 17:37:25,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce50194-1374-494c-87c0-c8884c63fc58/GCF_017979375.1_ASM1797937v1_genomic.fna.gz --refList GCF_017979375.1_ASM1797937v1_genomic.fna/target_genomes.txt --output GCF_017979375.1_ASM1797937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:28,434] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:28,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:28,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:28,441] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:37:28,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:28,441] [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 suis	strain=DSM 19735	GCA_017979375.1	104628	104628	type	True	100.0	489	493	95	conclusive
Helicobacter suis	strain=HS1	GCA_000187625.2	104628	104628	type	True	99.9437	483	493	95	conclusive
Helicobacter ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	77.6938	122	493	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	77.4874	147	493	95	below_threshold
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	77.1369	111	493	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	77.078	108	493	95	below_threshold
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	77.0363	94	493	95	below_threshold
Helicobacter pylori	strain=CCUG 17874	GCA_000258845.1	210	210	type	True	76.3489	54	493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:28,443] [INFO] DFAST Taxonomy check result was written to GCF_017979375.1_ASM1797937v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:28,444] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:28,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:28,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/checkm_data
[2024-01-25 17:37:28,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:28,463] [INFO] Task started: CheckM
[2024-01-25 17:37:28,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017979375.1_ASM1797937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017979375.1_ASM1797937v1_genomic.fna/checkm_input GCF_017979375.1_ASM1797937v1_genomic.fna/checkm_result
[2024-01-25 17:37:43,089] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:43,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:43,110] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:43,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:43,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017979375.1_ASM1797937v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:43,111] [INFO] Task started: Blastn
[2024-01-25 17:37:43,111] [INFO] Running command: blastn -query GCF_017979375.1_ASM1797937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daf64e8-ab9f-449f-8794-227cf366e46e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017979375.1_ASM1797937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:43,879] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:43,882] [INFO] Selected 9 target genomes.
[2024-01-25 17:37:43,882] [INFO] Target genome list was writen to GCF_017979375.1_ASM1797937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:43,912] [INFO] Task started: fastANI
[2024-01-25 17:37:43,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce50194-1374-494c-87c0-c8884c63fc58/GCF_017979375.1_ASM1797937v1_genomic.fna.gz --refList GCF_017979375.1_ASM1797937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017979375.1_ASM1797937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:46,989] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:46,996] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:46,996] [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_000187625.1	s__Helicobacter_E suis	99.9437	483	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.74	99.56	0.96	0.89	27	conclusive
GCF_902196135.1	s__Helicobacter_E suis_A	93.7946	443	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.68	97.34	0.95	0.91	4	-
GCF_902196125.1	s__Helicobacter_E suis_B	91.9376	445	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	96.42	96.42	0.94	0.90	3	-
GCF_000259255.1	s__Helicobacter cetorum_B	78.6495	61	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	96.46	95.82	0.94	0.93	3	-
GCF_001282945.1	s__Helicobacter_E ailurogastricus	77.6938	122	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.41	98.32	0.95	0.92	6	-
GCF_003660265.1	s__Helicobacter_E mehlei	77.5089	146	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.56	99.56	0.97	0.96	3	-
GCF_900197855.1	s__Helicobacter_E cynogastricus	77.4206	110	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001283065.1	s__Helicobacter_E heilmannii	77.1369	111	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.65	98.18	0.97	0.95	9	-
GCF_017979425.1	s__Helicobacter_E salomonis	77.0363	94	493	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.86	98.52	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:46,998] [INFO] GTDB search result was written to GCF_017979375.1_ASM1797937v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:46,999] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:47,001] [INFO] DFAST_QC result json was written to GCF_017979375.1_ASM1797937v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:47,002] [INFO] DFAST_QC completed!
[2024-01-25 17:37:47,002] [INFO] Total running time: 0h0m26s