[2024-01-24 15:26:54,184] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference
[2024-01-24 15:26:55,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:55,597] [INFO] Task started: Prodigal
[2024-01-24 15:26:55,597] [INFO] Running command: gunzip -c /var/lib/cwl/stgcafdc9ba-5945-4154-97b2-2c128057bba4/GCF_016593255.1_ASM1659325v1_genomic.fna.gz | prodigal -d GCF_016593255.1_ASM1659325v1_genomic.fna/cds.fna -a GCF_016593255.1_ASM1659325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:02,796] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:02,797] [INFO] Task started: HMMsearch
[2024-01-24 15:27:02,797] [INFO] Running command: hmmsearch --tblout GCF_016593255.1_ASM1659325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/reference_markers.hmm GCF_016593255.1_ASM1659325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:03,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:03,037] [INFO] Found 6/6 markers.
[2024-01-24 15:27:03,060] [INFO] Query marker FASTA was written to GCF_016593255.1_ASM1659325v1_genomic.fna/markers.fasta
[2024-01-24 15:27:03,060] [INFO] Task started: Blastn
[2024-01-24 15:27:03,061] [INFO] Running command: blastn -query GCF_016593255.1_ASM1659325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/reference_markers.fasta -out GCF_016593255.1_ASM1659325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:03,720] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:03,723] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:03,724] [INFO] Target genome list was writen to GCF_016593255.1_ASM1659325v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:03,794] [INFO] Task started: fastANI
[2024-01-24 15:27:03,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgcafdc9ba-5945-4154-97b2-2c128057bba4/GCF_016593255.1_ASM1659325v1_genomic.fna.gz --refList GCF_016593255.1_ASM1659325v1_genomic.fna/target_genomes.txt --output GCF_016593255.1_ASM1659325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:13,390] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:13,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:13,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:13,396] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:13,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:13,396] [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
Hydrogenimonas urashimensis	strain=SSM-sur55	GCA_016593255.1	2740515	2740515	type	True	100.0	765	765	95	conclusive
Hydrogenimonas thermophila	strain=EP1-55-1	GCA_900115615.1	223786	223786	type	True	77.9876	52	765	95	below_threshold
Nitratifractor salsuginis	strain=DSM 16511	GCA_000186245.1	269261	269261	type	True	77.5344	102	765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:13,398] [INFO] DFAST Taxonomy check result was written to GCF_016593255.1_ASM1659325v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:13,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:13,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:13,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/checkm_data
[2024-01-24 15:27:13,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:13,424] [INFO] Task started: CheckM
[2024-01-24 15:27:13,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016593255.1_ASM1659325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016593255.1_ASM1659325v1_genomic.fna/checkm_input GCF_016593255.1_ASM1659325v1_genomic.fna/checkm_result
[2024-01-24 15:27:39,819] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:39,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:39,836] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:39,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:39,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016593255.1_ASM1659325v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:39,837] [INFO] Task started: Blastn
[2024-01-24 15:27:39,837] [INFO] Running command: blastn -query GCF_016593255.1_ASM1659325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66d9534b-35d2-442f-b576-422a63126762/dqc_reference/reference_markers_gtdb.fasta -out GCF_016593255.1_ASM1659325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:40,714] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:40,718] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:40,718] [INFO] Target genome list was writen to GCF_016593255.1_ASM1659325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:40,731] [INFO] Task started: fastANI
[2024-01-24 15:27:40,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgcafdc9ba-5945-4154-97b2-2c128057bba4/GCF_016593255.1_ASM1659325v1_genomic.fna.gz --refList GCF_016593255.1_ASM1659325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016593255.1_ASM1659325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:47,439] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:47,451] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:47,452] [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_016593255.1	s__Hydrogenimonas urashimensis	100.0	765	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013153475.1	s__Hydrogenimonas sp013153475	77.9972	187	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115615.1	s__Hydrogenimonas thermophila	77.9876	52	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003945285.1	s__Hydrogenimonas sp003945285	77.8711	171	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186245.1	s__Nitratifractor salsuginis	77.5295	102	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Nitratifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490295.1	s__Hydrogenimonas sp015490295	77.4454	129	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015486995.1	s__Nitratifractor sp015486995	77.3058	73	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Nitratifractor	95.0	95.88	95.24	0.75	0.68	3	-
GCA_015494675.1	s__Hydrogenimonas sp015494675	77.1505	122	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487065.1	s__Nitratifractor sp015487065	76.6604	77	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Nitratifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978765.1	s__Hydrogenimonas sp003978765	76.6335	77	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Hydrogenimonadaceae;g__Hydrogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245815.1	s__SZUA-415 sp003245815	76.1039	68	765	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__SZUA-415	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:47,454] [INFO] GTDB search result was written to GCF_016593255.1_ASM1659325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:47,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:47,462] [INFO] DFAST_QC result json was written to GCF_016593255.1_ASM1659325v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:47,462] [INFO] DFAST_QC completed!
[2024-01-24 15:27:47,462] [INFO] Total running time: 0h0m53s