[2024-01-24 12:06:21,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:21,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:21,681] [INFO] DQC Reference Directory: /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference
[2024-01-24 12:06:22,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:22,943] [INFO] Task started: Prodigal
[2024-01-24 12:06:22,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg1311449c-81a8-4aad-ae2f-42d54e985397/GCF_025998455.1_ASM2599845v1_genomic.fna.gz | prodigal -d GCF_025998455.1_ASM2599845v1_genomic.fna/cds.fna -a GCF_025998455.1_ASM2599845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,813] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,813] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,814] [INFO] Running command: hmmsearch --tblout GCF_025998455.1_ASM2599845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/reference_markers.hmm GCF_025998455.1_ASM2599845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,032] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,049] [INFO] Query marker FASTA was written to GCF_025998455.1_ASM2599845v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,050] [INFO] Task started: Blastn
[2024-01-24 12:06:27,050] [INFO] Running command: blastn -query GCF_025998455.1_ASM2599845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/reference_markers.fasta -out GCF_025998455.1_ASM2599845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,621] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,624] [INFO] Selected 6 target genomes.
[2024-01-24 12:06:27,624] [INFO] Target genome list was writen to GCF_025998455.1_ASM2599845v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,627] [INFO] Task started: fastANI
[2024-01-24 12:06:27,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg1311449c-81a8-4aad-ae2f-42d54e985397/GCF_025998455.1_ASM2599845v1_genomic.fna.gz --refList GCF_025998455.1_ASM2599845v1_genomic.fna/target_genomes.txt --output GCF_025998455.1_ASM2599845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:30,173] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:30,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:30,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:30,181] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:30,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:30,181] [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 pylori	strain=ATCC 43504	GCA_004295525.1	210	210	type	True	94.9788	514	565	95	below_threshold
Helicobacter pylori	strain=NCTC 11637	GCA_900478295.1	210	210	type	True	94.9481	516	565	95	below_threshold
Helicobacter pylori	strain=FDAARGOS_298	GCA_003050665.1	210	210	type	True	94.8733	513	565	95	below_threshold
Helicobacter pylori	strain=CCUG 17874	GCA_000258845.1	210	210	type	True	94.6886	418	565	95	below_threshold
Helicobacter pylori	strain=JCM 12093	GCA_014654435.1	210	210	type	True	94.5107	454	565	95	below_threshold
Helicobacter acinonychis	strain=NCTC12686	GCA_900461455.1	212	212	type	True	89.6709	457	565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:30,182] [INFO] DFAST Taxonomy check result was written to GCF_025998455.1_ASM2599845v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:30,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:30,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:30,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/checkm_data
[2024-01-24 12:06:30,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:30,209] [INFO] Task started: CheckM
[2024-01-24 12:06:30,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025998455.1_ASM2599845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025998455.1_ASM2599845v1_genomic.fna/checkm_input GCF_025998455.1_ASM2599845v1_genomic.fna/checkm_result
[2024-01-24 12:06:48,869] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:48,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:48,891] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:48,891] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:48,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025998455.1_ASM2599845v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:48,891] [INFO] Task started: Blastn
[2024-01-24 12:06:48,891] [INFO] Running command: blastn -query GCF_025998455.1_ASM2599845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8641ef6-14d3-40b4-b555-513a8b87d0e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025998455.1_ASM2599845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,688] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,693] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:49,693] [INFO] Target genome list was writen to GCF_025998455.1_ASM2599845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:49,702] [INFO] Task started: fastANI
[2024-01-24 12:06:49,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg1311449c-81a8-4aad-ae2f-42d54e985397/GCF_025998455.1_ASM2599845v1_genomic.fna.gz --refList GCF_025998455.1_ASM2599845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025998455.1_ASM2599845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:53,050] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,060] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:06:53,060] [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_000277405.1	s__Helicobacter pylori_C	96.0574	518	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.2184	96.43	95.23	0.96	0.89	435	inconclusive
GCF_009689985.1	s__Helicobacter pylori_CG	95.451	490	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.2184	95.73	95.28	0.94	0.91	8	inconclusive
GCF_001653475.1	s__Helicobacter pylori_CM	95.122	489	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1561	95.99	95.99	0.96	0.96	2	-
GCF_900478295.1	s__Helicobacter pylori	94.9355	516	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1033	95.74	95.20	0.96	0.89	759	-
GCF_003637665.1	s__Helicobacter pylori_CK	94.4055	489	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0255	95.54	95.27	0.95	0.93	16	-
GCF_000476275.1	s__Helicobacter pylori_CL	94.125	468	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0096	99.99	99.99	0.99	0.99	2	-
GCF_003637685.1	s__Helicobacter pylori_CJ	94.0512	481	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1579	95.67	95.36	0.94	0.91	66	-
GCF_000448485.1	s__Helicobacter pylori_CI	93.8454	402	565	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0968	95.60	95.24	0.92	0.84	283	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,062] [INFO] GTDB search result was written to GCF_025998455.1_ASM2599845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:53,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:53,079] [INFO] DFAST_QC result json was written to GCF_025998455.1_ASM2599845v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:53,079] [INFO] DFAST_QC completed!
[2024-01-24 12:06:53,080] [INFO] Total running time: 0h0m31s