[2024-01-24 11:43:40,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,598] [INFO] DQC Reference Directory: /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference
[2024-01-24 11:43:41,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:41,875] [INFO] Task started: Prodigal
[2024-01-24 11:43:41,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f67f7a7-3801-4432-af04-4274baf1bb2a/GCF_003364335.1_ASM336433v1_genomic.fna.gz | prodigal -d GCF_003364335.1_ASM336433v1_genomic.fna/cds.fna -a GCF_003364335.1_ASM336433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:45,105] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:45,105] [INFO] Task started: HMMsearch
[2024-01-24 11:43:45,106] [INFO] Running command: hmmsearch --tblout GCF_003364335.1_ASM336433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/reference_markers.hmm GCF_003364335.1_ASM336433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:45,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:45,407] [INFO] Found 6/6 markers.
[2024-01-24 11:43:45,426] [INFO] Query marker FASTA was written to GCF_003364335.1_ASM336433v1_genomic.fna/markers.fasta
[2024-01-24 11:43:45,426] [INFO] Task started: Blastn
[2024-01-24 11:43:45,426] [INFO] Running command: blastn -query GCF_003364335.1_ASM336433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/reference_markers.fasta -out GCF_003364335.1_ASM336433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:46,034] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:46,037] [INFO] Selected 21 target genomes.
[2024-01-24 11:43:46,038] [INFO] Target genome list was writen to GCF_003364335.1_ASM336433v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:46,199] [INFO] Task started: fastANI
[2024-01-24 11:43:46,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f67f7a7-3801-4432-af04-4274baf1bb2a/GCF_003364335.1_ASM336433v1_genomic.fna.gz --refList GCF_003364335.1_ASM336433v1_genomic.fna/target_genomes.txt --output GCF_003364335.1_ASM336433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:53,591] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:53,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:53,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:53,598] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:53,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:53,598] [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 anseris	strain=MIT 04-9362	GCA_003364335.1	375926	375926	type	True	100.0	518	520	95	conclusive
Helicobacter anatolicus	strain=faydin-H8	GCA_021300615.1	2905874	2905874	type	True	78.0358	164	520	95	below_threshold
Helicobacter cholecystus	strain=ATCC 700242	GCA_003364215.1	45498	45498	type	True	77.8339	52	520	95	below_threshold
Helicobacter kayseriensis	strain=faydin-H23	GCA_021300655.1	2905877	2905877	type	True	77.3583	52	520	95	below_threshold
Helicobacter valdiviensis	strain=WBE14	GCA_003245365.1	1458358	1458358	type	True	76.8906	58	520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:53,600] [INFO] DFAST Taxonomy check result was written to GCF_003364335.1_ASM336433v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:53,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:53,601] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:53,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/checkm_data
[2024-01-24 11:43:53,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:53,624] [INFO] Task started: CheckM
[2024-01-24 11:43:53,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003364335.1_ASM336433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003364335.1_ASM336433v1_genomic.fna/checkm_input GCF_003364335.1_ASM336433v1_genomic.fna/checkm_result
[2024-01-24 11:44:11,758] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:11,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:11,776] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:11,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:11,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003364335.1_ASM336433v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:11,776] [INFO] Task started: Blastn
[2024-01-24 11:44:11,777] [INFO] Running command: blastn -query GCF_003364335.1_ASM336433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge144b712-8953-4fe1-9a23-5ca483c44651/dqc_reference/reference_markers_gtdb.fasta -out GCF_003364335.1_ASM336433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:12,643] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:12,647] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:12,647] [INFO] Target genome list was writen to GCF_003364335.1_ASM336433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:12,676] [INFO] Task started: fastANI
[2024-01-24 11:44:12,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f67f7a7-3801-4432-af04-4274baf1bb2a/GCF_003364335.1_ASM336433v1_genomic.fna.gz --refList GCF_003364335.1_ASM336433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003364335.1_ASM336433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:20,037] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:20,045] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:20,045] [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_003364335.1	s__Helicobacter_H anseris	100.0	518	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900199585.1	s__Helicobacter_H sp900199585	78.6824	248	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003364215.1	s__Helicobacter_G cholecystus	77.8339	52	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G	95.0	99.98	99.98	0.99	0.98	3	-
GCF_004368235.1	s__Helicobacter_H anseris_A	77.4139	95	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272895.1	s__Helicobacter_J sp002272895	77.2914	60	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272795.1	s__Helicobacter_J sp002272795	77.0519	65	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272785.1	s__Helicobacter_J sp002272785	76.9285	67	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272835.1	s__Helicobacter_J sp002272835	76.9191	75	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:20,047] [INFO] GTDB search result was written to GCF_003364335.1_ASM336433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:20,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:20,052] [INFO] DFAST_QC result json was written to GCF_003364335.1_ASM336433v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:20,052] [INFO] DFAST_QC completed!
[2024-01-24 11:44:20,052] [INFO] Total running time: 0h0m39s