[2024-01-24 12:31:33,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference
[2024-01-24 12:31:35,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,249] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg087fa101-010a-4d75-a1ae-4e75ca5ea566/GCF_000158455.1_ASM15845v1_genomic.fna.gz | prodigal -d GCF_000158455.1_ASM15845v1_genomic.fna/cds.fna -a GCF_000158455.1_ASM15845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:39,061] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:39,061] [INFO] Task started: HMMsearch
[2024-01-24 12:31:39,061] [INFO] Running command: hmmsearch --tblout GCF_000158455.1_ASM15845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/reference_markers.hmm GCF_000158455.1_ASM15845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:39,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:39,280] [INFO] Found 6/6 markers.
[2024-01-24 12:31:39,303] [INFO] Query marker FASTA was written to GCF_000158455.1_ASM15845v1_genomic.fna/markers.fasta
[2024-01-24 12:31:39,304] [INFO] Task started: Blastn
[2024-01-24 12:31:39,304] [INFO] Running command: blastn -query GCF_000158455.1_ASM15845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/reference_markers.fasta -out GCF_000158455.1_ASM15845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,958] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,966] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:39,966] [INFO] Target genome list was writen to GCF_000158455.1_ASM15845v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:39,973] [INFO] Task started: fastANI
[2024-01-24 12:31:39,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg087fa101-010a-4d75-a1ae-4e75ca5ea566/GCF_000158455.1_ASM15845v1_genomic.fna.gz --refList GCF_000158455.1_ASM15845v1_genomic.fna/target_genomes.txt --output GCF_000158455.1_ASM15845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:43,779] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:43,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:43,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:43,789] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:43,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:43,790] [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 winghamensis	strain=ATCC BAA-430	GCA_000158455.1	157268	157268	type	True	99.9996	552	555	95	conclusive
Helicobacter turcicus	strain=Faydin-H70	GCA_019711685.1	2867412	2867412	type	True	81.5995	420	555	95	below_threshold
Helicobacter rodentium	strain=ATCC 700285	GCA_000687535.1	59617	59617	type	True	78.7671	249	555	95	below_threshold
Helicobacter pullorum	strain=CCUG 33837	GCA_017979475.1	35818	35818	type	True	78.4586	193	555	95	below_threshold
Helicobacter valdiviensis	strain=WBE14	GCA_003245365.1	1458358	1458358	type	True	78.1425	186	555	95	below_threshold
Helicobacter canadensis	strain=MIT 98-5491	GCA_000155455.1	123841	123841	type	True	78.0155	187	555	95	below_threshold
Helicobacter burdigaliensis	strain=CNRCH 2005/566H	GCA_003670295.1	2315334	2315334	type	True	78.0011	199	555	95	below_threshold
Helicobacter canadensis	strain=MIT 98-5491	GCA_000162575.1	123841	123841	type	True	77.9867	189	555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,793] [INFO] DFAST Taxonomy check result was written to GCF_000158455.1_ASM15845v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:43,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:43,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:43,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/checkm_data
[2024-01-24 12:31:43,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:43,818] [INFO] Task started: CheckM
[2024-01-24 12:31:43,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000158455.1_ASM15845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000158455.1_ASM15845v1_genomic.fna/checkm_input GCF_000158455.1_ASM15845v1_genomic.fna/checkm_result
[2024-01-24 12:32:01,723] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:01,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,742] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:01,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:01,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000158455.1_ASM15845v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:01,743] [INFO] Task started: Blastn
[2024-01-24 12:32:01,743] [INFO] Running command: blastn -query GCF_000158455.1_ASM15845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f8fa53-462b-446c-9d21-95c8545e3a76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000158455.1_ASM15845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:02,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:02,568] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:02,569] [INFO] Target genome list was writen to GCF_000158455.1_ASM15845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:02,577] [INFO] Task started: fastANI
[2024-01-24 12:32:02,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg087fa101-010a-4d75-a1ae-4e75ca5ea566/GCF_000158455.1_ASM15845v1_genomic.fna.gz --refList GCF_000158455.1_ASM15845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000158455.1_ASM15845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:07,188] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,199] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:07,199] [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_000158455.1	s__Helicobacter_D winghamensis	99.9996	552	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.73	99.12	0.98	0.96	8	conclusive
GCF_000765695.2	s__Helicobacter_D sp000765695	81.3473	383	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687535.1	s__Helicobacter_D rodentium	78.7671	249	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	98.53	98.53	0.90	0.90	2	-
GCF_008801855.1	s__Helicobacter_D pullorum	78.3822	195	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	97.98	97.63	0.93	0.87	29	-
GCF_003364315.1	s__Helicobacter_D ganmani	78.2841	213	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.45	99.17	0.96	0.93	4	-
GCF_003288905.1	s__Helicobacter_D sp003288905	78.1719	178	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003245365.1	s__Helicobacter_D valdiviensis	78.1425	186	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765675.1	s__Helicobacter_D sp000765675	78.0812	217	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000162575.1	s__Helicobacter_D canadensis	78.0554	190	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	99.98	99.92	1.00	0.99	5	-
GCA_014799995.1	s__Helicobacter_D sp014799995	77.8779	217	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765745.2	s__Helicobacter_D apodemus	77.7611	150	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D	95.0	98.27	97.09	0.93	0.91	3	-
GCF_000007905.1	s__Helicobacter_C hepaticus	76.8178	57	555	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	98.74	98.74	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,203] [INFO] GTDB search result was written to GCF_000158455.1_ASM15845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:07,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:07,232] [INFO] DFAST_QC result json was written to GCF_000158455.1_ASM15845v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:07,233] [INFO] DFAST_QC completed!
[2024-01-24 12:32:07,233] [INFO] Total running time: 0h0m33s