[2024-01-25 17:43:20,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:20,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:20,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference
[2024-01-25 17:43:21,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:21,778] [INFO] Task started: Prodigal
[2024-01-25 17:43:21,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg9af0bc34-a28f-4c7f-85e8-1376be2fd2f3/GCF_016726265.1_ASM1672626v1_genomic.fna.gz | prodigal -d GCF_016726265.1_ASM1672626v1_genomic.fna/cds.fna -a GCF_016726265.1_ASM1672626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:24,228] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:24,228] [INFO] Task started: HMMsearch
[2024-01-25 17:43:24,228] [INFO] Running command: hmmsearch --tblout GCF_016726265.1_ASM1672626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/reference_markers.hmm GCF_016726265.1_ASM1672626v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:24,436] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:24,437] [INFO] Found 6/6 markers.
[2024-01-25 17:43:24,456] [INFO] Query marker FASTA was written to GCF_016726265.1_ASM1672626v1_genomic.fna/markers.fasta
[2024-01-25 17:43:24,456] [INFO] Task started: Blastn
[2024-01-25 17:43:24,456] [INFO] Running command: blastn -query GCF_016726265.1_ASM1672626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/reference_markers.fasta -out GCF_016726265.1_ASM1672626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:25,024] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:25,027] [INFO] Selected 5 target genomes.
[2024-01-25 17:43:25,027] [INFO] Target genome list was writen to GCF_016726265.1_ASM1672626v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:25,057] [INFO] Task started: fastANI
[2024-01-25 17:43:25,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af0bc34-a28f-4c7f-85e8-1376be2fd2f3/GCF_016726265.1_ASM1672626v1_genomic.fna.gz --refList GCF_016726265.1_ASM1672626v1_genomic.fna/target_genomes.txt --output GCF_016726265.1_ASM1672626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:27,083] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:27,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:27,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:27,089] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 17:43:27,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:27,089] [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
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	100.0	503	504	95	conclusive
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	99.9992	501	504	95	conclusive
Campylobacter lari subsp. lari	strain=LMG 8846	GCA_013372185.1	650054	201	type	True	99.9986	501	504	95	conclusive
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	99.9123	481	504	95	conclusive
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	93.2965	449	504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:27,090] [INFO] DFAST Taxonomy check result was written to GCF_016726265.1_ASM1672626v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:27,091] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:27,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:27,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/checkm_data
[2024-01-25 17:43:27,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:27,113] [INFO] Task started: CheckM
[2024-01-25 17:43:27,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016726265.1_ASM1672626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016726265.1_ASM1672626v1_genomic.fna/checkm_input GCF_016726265.1_ASM1672626v1_genomic.fna/checkm_result
[2024-01-25 17:43:40,854] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:40,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:40,872] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:40,872] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:40,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016726265.1_ASM1672626v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:40,873] [INFO] Task started: Blastn
[2024-01-25 17:43:40,873] [INFO] Running command: blastn -query GCF_016726265.1_ASM1672626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7ce5bc9-9c31-4c2f-ab7f-03354f33a738/dqc_reference/reference_markers_gtdb.fasta -out GCF_016726265.1_ASM1672626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:41,651] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:41,655] [INFO] Selected 5 target genomes.
[2024-01-25 17:43:41,655] [INFO] Target genome list was writen to GCF_016726265.1_ASM1672626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:41,666] [INFO] Task started: fastANI
[2024-01-25 17:43:41,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af0bc34-a28f-4c7f-85e8-1376be2fd2f3/GCF_016726265.1_ASM1672626v1_genomic.fna.gz --refList GCF_016726265.1_ASM1672626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016726265.1_ASM1672626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:43,709] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:43,714] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:43,714] [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_013372185.1	s__Campylobacter_D lari	99.9986	501	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.73	98.09	0.96	0.93	13	conclusive
GCF_008245025.1	s__Campylobacter_D concheus	93.2965	449	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.27	98.88	0.96	0.94	4	-
GCF_001017575.1	s__Campylobacter_D lari_C	92.6856	459	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.15	95.06	0.92	0.89	21	-
GCF_002179635.1	s__Campylobacter_D jejuni_C	92.2515	416	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.56	98.44	0.93	0.93	4	-
GCF_004357905.1	s__Campylobacter_D lari_D	91.728	430	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:43,716] [INFO] GTDB search result was written to GCF_016726265.1_ASM1672626v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:43,716] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:43,718] [INFO] DFAST_QC result json was written to GCF_016726265.1_ASM1672626v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:43,719] [INFO] DFAST_QC completed!
[2024-01-25 17:43:43,719] [INFO] Total running time: 0h0m23s