[2024-01-24 13:13:39,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference
[2024-01-24 13:13:40,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,634] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg1db5f232-b63b-437a-bf52-e0daa8689708/GCF_003364255.1_ASM336425v1_genomic.fna.gz | prodigal -d GCF_003364255.1_ASM336425v1_genomic.fna/cds.fna -a GCF_003364255.1_ASM336425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:45,244] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:45,244] [INFO] Task started: HMMsearch
[2024-01-24 13:13:45,244] [INFO] Running command: hmmsearch --tblout GCF_003364255.1_ASM336425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/reference_markers.hmm GCF_003364255.1_ASM336425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:45,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:45,456] [INFO] Found 6/6 markers.
[2024-01-24 13:13:45,476] [INFO] Query marker FASTA was written to GCF_003364255.1_ASM336425v1_genomic.fna/markers.fasta
[2024-01-24 13:13:45,477] [INFO] Task started: Blastn
[2024-01-24 13:13:45,477] [INFO] Running command: blastn -query GCF_003364255.1_ASM336425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/reference_markers.fasta -out GCF_003364255.1_ASM336425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:46,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:46,091] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:46,091] [INFO] Target genome list was writen to GCF_003364255.1_ASM336425v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:46,114] [INFO] Task started: fastANI
[2024-01-24 13:13:46,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db5f232-b63b-437a-bf52-e0daa8689708/GCF_003364255.1_ASM336425v1_genomic.fna.gz --refList GCF_003364255.1_ASM336425v1_genomic.fna/target_genomes.txt --output GCF_003364255.1_ASM336425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:50,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:50,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:50,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:50,580] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:50,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:50,580] [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 marmotae	strain=MIT 98-6070	GCA_003364255.1	152490	152490	type	True	100.0	625	626	95	conclusive
Helicobacter japonicus	strain=MIT 01-6451	GCA_000762845.2	425400	425400	type	True	78.3051	257	626	95	below_threshold
Helicobacter labetoulli	strain=48519	GCA_003670275.1	2315333	2315333	type	True	78.1271	237	626	95	below_threshold
Helicobacter cinaedi	strain=CCUG 18818	GCA_003215615.1	213	213	type	True	78.0802	250	626	95	below_threshold
Helicobacter cinaedi	strain=DSM 5359	GCA_017979495.1	213	213	type	True	78.0043	256	626	95	below_threshold
Helicobacter cinaedi	strain=ATCC BAA-847	GCA_000349975.1	213	213	type	True	77.9718	261	626	95	below_threshold
Helicobacter jaachi	strain=MIT 09-6949	GCA_000763135.2	1677920	1677920	type	True	77.9633	236	626	95	below_threshold
Helicobacter cinaedi	strain=CCUG 18818	GCA_000155475.1	213	213	type	True	77.8398	266	626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,582] [INFO] DFAST Taxonomy check result was written to GCF_003364255.1_ASM336425v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:50,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:50,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:50,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/checkm_data
[2024-01-24 13:13:50,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:50,605] [INFO] Task started: CheckM
[2024-01-24 13:13:50,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003364255.1_ASM336425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003364255.1_ASM336425v1_genomic.fna/checkm_input GCF_003364255.1_ASM336425v1_genomic.fna/checkm_result
[2024-01-24 13:14:11,292] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:11,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,310] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:11,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:11,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003364255.1_ASM336425v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:11,311] [INFO] Task started: Blastn
[2024-01-24 13:14:11,311] [INFO] Running command: blastn -query GCF_003364255.1_ASM336425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg389930bf-5124-4c8d-b163-1e9c84c3e036/dqc_reference/reference_markers_gtdb.fasta -out GCF_003364255.1_ASM336425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:12,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:12,122] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:12,122] [INFO] Target genome list was writen to GCF_003364255.1_ASM336425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:12,130] [INFO] Task started: fastANI
[2024-01-24 13:14:12,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db5f232-b63b-437a-bf52-e0daa8689708/GCF_003364255.1_ASM336425v1_genomic.fna.gz --refList GCF_003364255.1_ASM336425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003364255.1_ASM336425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:17,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:17,034] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:17,034] [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_003364255.1	s__Helicobacter_C marmotae	100.0	625	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCA_910577135.1	s__Helicobacter_C sp910577135	78.5636	305	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765825.2	s__Helicobacter_C magdeburgensis	78.3357	247	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	96.93	95.65	0.89	0.84	5	-
GCF_000762845.2	s__Helicobacter_C japonicus	78.2904	258	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001460635.1	s__Helicobacter_C typhlonius	78.2792	258	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.68	99.28	0.98	0.97	7	-
GCF_003670275.1	s__Helicobacter_C labetoulli	78.1271	237	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007905.1	s__Helicobacter_C hepaticus	78.0998	243	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	98.74	98.74	0.96	0.95	3	-
GCF_000763135.2	s__Helicobacter_C jaachi	77.9633	236	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155475.1	s__Helicobacter_C cinaedi	77.8514	265	626	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.33	98.84	0.97	0.91	38	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:17,036] [INFO] GTDB search result was written to GCF_003364255.1_ASM336425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:17,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:17,039] [INFO] DFAST_QC result json was written to GCF_003364255.1_ASM336425v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:17,039] [INFO] DFAST_QC completed!
[2024-01-24 13:14:17,040] [INFO] Total running time: 0h0m38s