[2024-01-24 10:48:09,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a57d75a-60dd-448f-a744-07b3043ba3af/GCF_003660285.1_ASM366028v1_genomic.fna.gz | prodigal -d GCF_003660285.1_ASM366028v1_genomic.fna/cds.fna -a GCF_003660285.1_ASM366028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:28,682] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:28,682] [INFO] Task started: HMMsearch
[2024-01-24 10:48:28,683] [INFO] Running command: hmmsearch --tblout GCF_003660285.1_ASM366028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/reference_markers.hmm GCF_003660285.1_ASM366028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:28,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:28,902] [INFO] Found 6/6 markers.
[2024-01-24 10:48:28,935] [INFO] Query marker FASTA was written to GCF_003660285.1_ASM366028v1_genomic.fna/markers.fasta
[2024-01-24 10:48:28,935] [INFO] Task started: Blastn
[2024-01-24 10:48:28,936] [INFO] Running command: blastn -query GCF_003660285.1_ASM366028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/reference_markers.fasta -out GCF_003660285.1_ASM366028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:29,555] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:29,561] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:29,561] [INFO] Target genome list was writen to GCF_003660285.1_ASM366028v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:29,567] [INFO] Task started: fastANI
[2024-01-24 10:48:29,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a57d75a-60dd-448f-a744-07b3043ba3af/GCF_003660285.1_ASM366028v1_genomic.fna.gz --refList GCF_003660285.1_ASM366028v1_genomic.fna/target_genomes.txt --output GCF_003660285.1_ASM366028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:32,310] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:32,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:32,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:32,318] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:32,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:32,318] [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 labacensis	strain=L9	GCA_003660285.1	2316079	2316079	type	True	100.0	542	544	95	conclusive
Helicobacter vulpis	strain=L2	GCA_003660395.1	2316076	2316076	type	True	83.5019	423	544	95	below_threshold
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	80.9099	304	544	95	below_threshold
Helicobacter felis	strain=ATCC 49179	GCA_000200595.1	214	214	type	True	80.4561	314	544	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	79.5044	248	544	95	below_threshold
Helicobacter ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	78.1965	202	544	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	77.8322	168	544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:32,320] [INFO] DFAST Taxonomy check result was written to GCF_003660285.1_ASM366028v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:32,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:32,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:32,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/checkm_data
[2024-01-24 10:48:32,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:32,342] [INFO] Task started: CheckM
[2024-01-24 10:48:32,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660285.1_ASM366028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660285.1_ASM366028v1_genomic.fna/checkm_input GCF_003660285.1_ASM366028v1_genomic.fna/checkm_result
[2024-01-24 10:48:54,569] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:54,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:54,588] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:54,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:54,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660285.1_ASM366028v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:54,590] [INFO] Task started: Blastn
[2024-01-24 10:48:54,590] [INFO] Running command: blastn -query GCF_003660285.1_ASM366028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08dadf53-77cd-4a62-9265-55557a777b74/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660285.1_ASM366028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:55,546] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:55,551] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:55,551] [INFO] Target genome list was writen to GCF_003660285.1_ASM366028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:55,616] [INFO] Task started: fastANI
[2024-01-24 10:48:55,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a57d75a-60dd-448f-a744-07b3043ba3af/GCF_003660285.1_ASM366028v1_genomic.fna.gz --refList GCF_003660285.1_ASM366028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660285.1_ASM366028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:59,503] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:59,511] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:59,511] [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_003660285.1	s__Helicobacter_E labacensis	100.0	542	544	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.30	98.30	0.89	0.89	2	conclusive
GCF_003660395.1	s__Helicobacter_E vulpis	83.5019	423	544	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_900197685.1	s__Helicobacter_E baculiformis	81.6596	308	544	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_017979425.1	s__Helicobacter_E salomonis	80.8539	308	544	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.86	98.52	0.94	0.92	6	-
GCF_000200595.1	s__Helicobacter_E felis	80.5039	311	544	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.57	97.30	0.96	0.93	23	-
GCF_900197855.1	s__Helicobacter_E cynogastricus	80.1381	283	544	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_003660265.1	s__Helicobacter_E mehlei	79.4848	249	544	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_001282945.1	s__Helicobacter_E ailurogastricus	78.191	203	544	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.41	98.32	0.95	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:59,514] [INFO] GTDB search result was written to GCF_003660285.1_ASM366028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:59,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:59,519] [INFO] DFAST_QC result json was written to GCF_003660285.1_ASM366028v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:59,519] [INFO] DFAST_QC completed!
[2024-01-24 10:48:59,519] [INFO] Total running time: 0h0m50s