[2024-01-24 12:36:23,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:23,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:23,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference
[2024-01-24 12:36:25,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,286] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,286] [INFO] Running command: gunzip -c /var/lib/cwl/stgf50f0ee7-39b0-448d-a21e-cdec2ea9fec8/GCF_008802155.1_ASM880215v1_genomic.fna.gz | prodigal -d GCF_008802155.1_ASM880215v1_genomic.fna/cds.fna -a GCF_008802155.1_ASM880215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:28,345] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:28,346] [INFO] Task started: HMMsearch
[2024-01-24 12:36:28,346] [INFO] Running command: hmmsearch --tblout GCF_008802155.1_ASM880215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/reference_markers.hmm GCF_008802155.1_ASM880215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:28,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:28,562] [INFO] Found 6/6 markers.
[2024-01-24 12:36:28,585] [INFO] Query marker FASTA was written to GCF_008802155.1_ASM880215v1_genomic.fna/markers.fasta
[2024-01-24 12:36:28,585] [INFO] Task started: Blastn
[2024-01-24 12:36:28,585] [INFO] Running command: blastn -query GCF_008802155.1_ASM880215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/reference_markers.fasta -out GCF_008802155.1_ASM880215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:29,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:29,173] [INFO] Selected 5 target genomes.
[2024-01-24 12:36:29,173] [INFO] Target genome list was writen to GCF_008802155.1_ASM880215v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:29,189] [INFO] Task started: fastANI
[2024-01-24 12:36:29,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50f0ee7-39b0-448d-a21e-cdec2ea9fec8/GCF_008802155.1_ASM880215v1_genomic.fna.gz --refList GCF_008802155.1_ASM880215v1_genomic.fna/target_genomes.txt --output GCF_008802155.1_ASM880215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:31,606] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:31,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:31,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:31,613] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:36:31,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:31,614] [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
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_008802155.1	28200	28200	type	True	100.0	637	639	95	conclusive
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_003544835.1	28200	28200	type	True	99.9984	638	639	95	conclusive
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	99.9982	639	639	95	conclusive
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	99.9975	638	639	95	conclusive
Aliarcobacter skirrowii	strain=NCTC12713	GCA_900445295.1	28200	28200	type	True	99.9884	637	639	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:36:31,616] [INFO] DFAST Taxonomy check result was written to GCF_008802155.1_ASM880215v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:31,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:31,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:31,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/checkm_data
[2024-01-24 12:36:31,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:31,642] [INFO] Task started: CheckM
[2024-01-24 12:36:31,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802155.1_ASM880215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802155.1_ASM880215v1_genomic.fna/checkm_input GCF_008802155.1_ASM880215v1_genomic.fna/checkm_result
[2024-01-24 12:36:48,761] [INFO] Task succeeded: CheckM
[2024-01-24 12:36:48,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:36:48,784] [INFO] ===== Completeness check finished =====
[2024-01-24 12:36:48,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:36:48,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802155.1_ASM880215v1_genomic.fna/markers.fasta)
[2024-01-24 12:36:48,785] [INFO] Task started: Blastn
[2024-01-24 12:36:48,785] [INFO] Running command: blastn -query GCF_008802155.1_ASM880215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93949735-fb09-4baf-b39b-0c2ee3745976/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802155.1_ASM880215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:49,606] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:49,610] [INFO] Selected 8 target genomes.
[2024-01-24 12:36:49,610] [INFO] Target genome list was writen to GCF_008802155.1_ASM880215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:49,622] [INFO] Task started: fastANI
[2024-01-24 12:36:49,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50f0ee7-39b0-448d-a21e-cdec2ea9fec8/GCF_008802155.1_ASM880215v1_genomic.fna.gz --refList GCF_008802155.1_ASM880215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802155.1_ASM880215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:53,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:53,434] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:53,434] [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_003544835.1	s__Aliarcobacter skirrowii	99.9984	638	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	conclusive
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	86.7217	473	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCA_017996075.1	s__Aliarcobacter sp017996075	85.9667	205	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	85.6954	456	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	84.7157	473	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004299785.2	s__Aliarcobacter porcinus	83.4945	474	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_004214815.1	s__Aliarcobacter thereius	83.3917	460	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013201705.1	s__Aliarcobacter faecis	82.4737	466	639	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:53,436] [INFO] GTDB search result was written to GCF_008802155.1_ASM880215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:53,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:53,439] [INFO] DFAST_QC result json was written to GCF_008802155.1_ASM880215v1_genomic.fna/dqc_result.json
[2024-01-24 12:36:53,439] [INFO] DFAST_QC completed!
[2024-01-24 12:36:53,439] [INFO] Total running time: 0h0m30s