[2024-01-24 13:55:19,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference
[2024-01-24 13:55:21,182] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,183] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg47c62fdd-a443-4e44-8fd5-9f7ea4474c32/GCF_000620965.1_ASM62096v1_genomic.fna.gz | prodigal -d GCF_000620965.1_ASM62096v1_genomic.fna/cds.fna -a GCF_000620965.1_ASM62096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:24,406] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:24,406] [INFO] Task started: HMMsearch
[2024-01-24 13:55:24,406] [INFO] Running command: hmmsearch --tblout GCF_000620965.1_ASM62096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/reference_markers.hmm GCF_000620965.1_ASM62096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:24,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:24,667] [INFO] Found 6/6 markers.
[2024-01-24 13:55:24,693] [INFO] Query marker FASTA was written to GCF_000620965.1_ASM62096v1_genomic.fna/markers.fasta
[2024-01-24 13:55:24,694] [INFO] Task started: Blastn
[2024-01-24 13:55:24,694] [INFO] Running command: blastn -query GCF_000620965.1_ASM62096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/reference_markers.fasta -out GCF_000620965.1_ASM62096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:25,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:25,291] [INFO] Selected 5 target genomes.
[2024-01-24 13:55:25,292] [INFO] Target genome list was writen to GCF_000620965.1_ASM62096v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:25,296] [INFO] Task started: fastANI
[2024-01-24 13:55:25,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c62fdd-a443-4e44-8fd5-9f7ea4474c32/GCF_000620965.1_ASM62096v1_genomic.fna.gz --refList GCF_000620965.1_ASM62096v1_genomic.fna/target_genomes.txt --output GCF_000620965.1_ASM62096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:27,393] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:27,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:27,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:27,400] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:27,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:27,400] [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	100.0	516	517	95	conclusive
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	99.9943	517	517	95	conclusive
Campylobacter upsaliensis	strain=NCTC11541	GCA_900637395.1	28080	28080	type	True	99.9939	516	517	95	conclusive
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	91.0757	436	517	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	86.2869	439	517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:27,402] [INFO] DFAST Taxonomy check result was written to GCF_000620965.1_ASM62096v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:27,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:27,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:27,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/checkm_data
[2024-01-24 13:55:27,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:27,423] [INFO] Task started: CheckM
[2024-01-24 13:55:27,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620965.1_ASM62096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620965.1_ASM62096v1_genomic.fna/checkm_input GCF_000620965.1_ASM62096v1_genomic.fna/checkm_result
[2024-01-24 13:55:44,981] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:44,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:45,007] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:45,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:45,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620965.1_ASM62096v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:45,009] [INFO] Task started: Blastn
[2024-01-24 13:55:45,009] [INFO] Running command: blastn -query GCF_000620965.1_ASM62096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bd42edd-f040-436a-a339-c2ae728383bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620965.1_ASM62096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:45,818] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:45,822] [INFO] Selected 9 target genomes.
[2024-01-24 13:55:45,822] [INFO] Target genome list was writen to GCF_000620965.1_ASM62096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:45,827] [INFO] Task started: fastANI
[2024-01-24 13:55:45,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c62fdd-a443-4e44-8fd5-9f7ea4474c32/GCF_000620965.1_ASM62096v1_genomic.fna.gz --refList GCF_000620965.1_ASM62096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620965.1_ASM62096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:49,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:49,192] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:49,193] [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	99.9939	516	517	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	91.0757	436	517	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	86.2869	439	517	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_000254135.1	s__Campylobacter_D coli	78.2056	223	517	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_002179165.1	s__Campylobacter_D jejuni_B	78.1569	245	517	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_001492295.1	s__Campylobacter_D coli_B	78.0189	234	517	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	77.9449	216	517	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	77.783	182	517	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	77.7649	224	517	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 13:55:49,195] [INFO] GTDB search result was written to GCF_000620965.1_ASM62096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:49,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:49,199] [INFO] DFAST_QC result json was written to GCF_000620965.1_ASM62096v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:49,199] [INFO] DFAST_QC completed!
[2024-01-24 13:55:49,199] [INFO] Total running time: 0h0m29s