[2024-01-24 13:31:44,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference
[2024-01-24 13:31:45,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,482] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg78217ffa-4687-4d62-906d-4f3740511d9b/GCF_030250085.1_ASM3025008v1_genomic.fna.gz | prodigal -d GCF_030250085.1_ASM3025008v1_genomic.fna/cds.fna -a GCF_030250085.1_ASM3025008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,706] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,707] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,707] [INFO] Running command: hmmsearch --tblout GCF_030250085.1_ASM3025008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/reference_markers.hmm GCF_030250085.1_ASM3025008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:49,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:49,021] [INFO] Found 6/6 markers.
[2024-01-24 13:31:49,047] [INFO] Query marker FASTA was written to GCF_030250085.1_ASM3025008v1_genomic.fna/markers.fasta
[2024-01-24 13:31:49,048] [INFO] Task started: Blastn
[2024-01-24 13:31:49,048] [INFO] Running command: blastn -query GCF_030250085.1_ASM3025008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/reference_markers.fasta -out GCF_030250085.1_ASM3025008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,637] [INFO] Selected 6 target genomes.
[2024-01-24 13:31:49,638] [INFO] Target genome list was writen to GCF_030250085.1_ASM3025008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,652] [INFO] Task started: fastANI
[2024-01-24 13:31:49,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg78217ffa-4687-4d62-906d-4f3740511d9b/GCF_030250085.1_ASM3025008v1_genomic.fna.gz --refList GCF_030250085.1_ASM3025008v1_genomic.fna/target_genomes.txt --output GCF_030250085.1_ASM3025008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:52,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:52,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:52,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:52,215] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:31:52,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:52,215] [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 upsaliensis	strain=DSM 5365	GCA_000620965.1	28080	28080	type	True	97.1274	491	549	95	conclusive
Campylobacter upsaliensis	strain=NCTC11541	GCA_900637395.1	28080	28080	type	True	96.9322	518	549	95	conclusive
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	96.926	519	549	95	conclusive
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	90.6647	453	549	95	below_threshold
Campylobacter helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	88.3384	445	549	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	88.3372	444	549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:52,217] [INFO] DFAST Taxonomy check result was written to GCF_030250085.1_ASM3025008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:52,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:52,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:52,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/checkm_data
[2024-01-24 13:31:52,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:52,242] [INFO] Task started: CheckM
[2024-01-24 13:31:52,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030250085.1_ASM3025008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030250085.1_ASM3025008v1_genomic.fna/checkm_input GCF_030250085.1_ASM3025008v1_genomic.fna/checkm_result
[2024-01-24 13:32:10,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:10,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:10,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:10,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:10,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030250085.1_ASM3025008v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:10,669] [INFO] Task started: Blastn
[2024-01-24 13:32:10,670] [INFO] Running command: blastn -query GCF_030250085.1_ASM3025008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ed42ab-8e4e-428a-9f3f-115b157471e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_030250085.1_ASM3025008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:11,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:11,537] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:11,537] [INFO] Target genome list was writen to GCF_030250085.1_ASM3025008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:11,556] [INFO] Task started: fastANI
[2024-01-24 13:32:11,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg78217ffa-4687-4d62-906d-4f3740511d9b/GCF_030250085.1_ASM3025008v1_genomic.fna.gz --refList GCF_030250085.1_ASM3025008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030250085.1_ASM3025008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:15,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:15,018] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:15,018] [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_900637395.1	s__Campylobacter_D upsaliensis	96.9322	518	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	96.80	95.96	0.91	0.88	18	conclusive
GCF_002738305.1	s__Campylobacter_D vulpis	90.6466	453	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.20	98.60	0.92	0.87	15	-
GCF_002080395.1	s__Campylobacter_D helveticus	88.3372	444	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.44	98.95	0.97	0.95	14	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	78.4077	234	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000254135.1	s__Campylobacter_D coli	78.3452	232	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.69	96.32	0.91	0.84	983	-
GCF_001492295.1	s__Campylobacter_D coli_B	78.2642	239	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.33	0.93	0.85	59	-
GCF_004378855.1	s__Campylobacter_D sp004378855	77.9265	212	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406215.1	s__Campylobacter_D aviculae	77.8939	194	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000470055.1	s__Campylobacter_D coli_A	77.8832	226	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.85	97.41	0.95	0.91	86	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:15,053] [INFO] GTDB search result was written to GCF_030250085.1_ASM3025008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:15,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:15,059] [INFO] DFAST_QC result json was written to GCF_030250085.1_ASM3025008v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:15,059] [INFO] DFAST_QC completed!
[2024-01-24 13:32:15,059] [INFO] Total running time: 0h0m31s