[2024-01-25 17:34:50,776] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:50,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:50,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference
[2024-01-25 17:34:51,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:51,930] [INFO] Task started: Prodigal
[2024-01-25 17:34:51,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4a91bb2-518f-4af1-91ec-4b9241910b61/GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna.gz | prodigal -d GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/cds.fna -a GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:57,003] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:57,003] [INFO] Task started: HMMsearch
[2024-01-25 17:34:57,003] [INFO] Running command: hmmsearch --tblout GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/reference_markers.hmm GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:57,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:57,208] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd4a91bb2-518f-4af1-91ec-4b9241910b61/GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna.gz]
[2024-01-25 17:34:57,228] [INFO] Query marker FASTA was written to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/markers.fasta
[2024-01-25 17:34:57,228] [INFO] Task started: Blastn
[2024-01-25 17:34:57,228] [INFO] Running command: blastn -query GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/reference_markers.fasta -out GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:57,829] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:57,837] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:57,837] [INFO] Target genome list was writen to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:57,842] [INFO] Task started: fastANI
[2024-01-25 17:34:57,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a91bb2-518f-4af1-91ec-4b9241910b61/GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna.gz --refList GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/target_genomes.txt --output GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:02,800] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:02,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:02,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:02,806] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:02,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:02,807] [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 macacae	strain=MIT 99-5501	GCA_000507845.1	398626	398626	type	True	99.9924	784	787	95	conclusive
Helicobacter cinaedi	strain=CCUG 18818	GCA_003215615.1	213	213	type	True	77.1852	64	787	95	below_threshold
Helicobacter himalayensis	strain=YS1	GCA_001602095.1	1591088	1591088	type	True	77.1584	75	787	95	below_threshold
Helicobacter canis	strain=CCUG 32756T	GCA_008693005.1	29419	29419	type	True	76.9184	126	787	95	below_threshold
Helicobacter canis	strain=CCUG 32756	GCA_017979455.1	29419	29419	type	True	76.6343	127	787	95	below_threshold
Helicobacter jaachi	strain=MIT 09-6949	GCA_000763135.2	1677920	1677920	type	True	76.347	64	787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:02,808] [INFO] DFAST Taxonomy check result was written to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:02,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:02,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:02,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/checkm_data
[2024-01-25 17:35:02,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:02,836] [INFO] Task started: CheckM
[2024-01-25 17:35:02,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/checkm_input GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/checkm_result
[2024-01-25 17:35:22,763] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:22,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:22,782] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:22,782] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:22,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/markers.fasta)
[2024-01-25 17:35:22,783] [INFO] Task started: Blastn
[2024-01-25 17:35:22,783] [INFO] Running command: blastn -query GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e8fee7-879e-4fb3-bc6e-eecef595d769/dqc_reference/reference_markers_gtdb.fasta -out GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:23,600] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:23,604] [INFO] Selected 13 target genomes.
[2024-01-25 17:35:23,604] [INFO] Target genome list was writen to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:23,613] [INFO] Task started: fastANI
[2024-01-25 17:35:23,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a91bb2-518f-4af1-91ec-4b9241910b61/GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna.gz --refList GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:29,625] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:29,630] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:29,630] [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_000507845.1	s__Helicobacter_B macacae	99.9924	784	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	97.58	95.16	0.95	0.91	3	conclusive
GCF_001602095.1	s__Helicobacter_F himalayensis	77.4054	75	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451095.1	s__Helicobacter_B canis_B	77.3717	140	787	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_001854545.1	s__Helicobacter_B sp001854545	77.2496	153	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.98	99.96	0.99	0.98	4	-
GCF_008693005.1	s__Helicobacter_B canis	76.8684	131	787	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	97.15	95.72	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:29,632] [INFO] GTDB search result was written to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:29,633] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:29,635] [INFO] DFAST_QC result json was written to GCF_000507845.1_Heli_maca_MIT_99-5501_V1_genomic.fna/dqc_result.json
[2024-01-25 17:35:29,635] [INFO] DFAST_QC completed!
[2024-01-25 17:35:29,635] [INFO] Total running time: 0h0m39s