[2024-01-24 11:12:39,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference
[2024-01-24 11:12:40,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,630] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg670dc949-c28c-4b79-b729-f11946cea78b/GCF_004803795.1_ASM480379v1_genomic.fna.gz | prodigal -d GCF_004803795.1_ASM480379v1_genomic.fna/cds.fna -a GCF_004803795.1_ASM480379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:45,980] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:45,980] [INFO] Task started: HMMsearch
[2024-01-24 11:12:45,980] [INFO] Running command: hmmsearch --tblout GCF_004803795.1_ASM480379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/reference_markers.hmm GCF_004803795.1_ASM480379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:46,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:46,213] [INFO] Found 6/6 markers.
[2024-01-24 11:12:46,235] [INFO] Query marker FASTA was written to GCF_004803795.1_ASM480379v1_genomic.fna/markers.fasta
[2024-01-24 11:12:46,236] [INFO] Task started: Blastn
[2024-01-24 11:12:46,236] [INFO] Running command: blastn -query GCF_004803795.1_ASM480379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/reference_markers.fasta -out GCF_004803795.1_ASM480379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:46,832] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:46,836] [INFO] Selected 8 target genomes.
[2024-01-24 11:12:46,836] [INFO] Target genome list was writen to GCF_004803795.1_ASM480379v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:46,879] [INFO] Task started: fastANI
[2024-01-24 11:12:46,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg670dc949-c28c-4b79-b729-f11946cea78b/GCF_004803795.1_ASM480379v1_genomic.fna.gz --refList GCF_004803795.1_ASM480379v1_genomic.fna/target_genomes.txt --output GCF_004803795.1_ASM480379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:51,697] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:51,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:51,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:51,705] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:51,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:51,706] [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 rectus	strain=ATCC 33238	GCA_004803795.1	203	203	type	True	100.0	854	857	95	conclusive
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	99.9977	856	857	95	conclusive
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	90.0018	616	857	95	below_threshold
Campylobacter showae	strain=ATCC 51146	GCA_004803815.1	204	204	suspected-type	True	89.173	591	857	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	78.7625	159	857	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	78.0903	220	857	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	76.6138	70	857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:51,707] [INFO] DFAST Taxonomy check result was written to GCF_004803795.1_ASM480379v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:51,708] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:51,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:51,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/checkm_data
[2024-01-24 11:12:51,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:51,744] [INFO] Task started: CheckM
[2024-01-24 11:12:51,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004803795.1_ASM480379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004803795.1_ASM480379v1_genomic.fna/checkm_input GCF_004803795.1_ASM480379v1_genomic.fna/checkm_result
[2024-01-24 11:13:14,225] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:14,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:14,253] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:14,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:14,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004803795.1_ASM480379v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:14,254] [INFO] Task started: Blastn
[2024-01-24 11:13:14,254] [INFO] Running command: blastn -query GCF_004803795.1_ASM480379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3abcdc89-b5cc-4b79-8b35-84582a0cac54/dqc_reference/reference_markers_gtdb.fasta -out GCF_004803795.1_ASM480379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,159] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,163] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:15,163] [INFO] Target genome list was writen to GCF_004803795.1_ASM480379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:15,171] [INFO] Task started: fastANI
[2024-01-24 11:13:15,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg670dc949-c28c-4b79-b729-f11946cea78b/GCF_004803795.1_ASM480379v1_genomic.fna.gz --refList GCF_004803795.1_ASM480379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004803795.1_ASM480379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:20,629] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,637] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:20,637] [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_004803795.1	s__Campylobacter_A rectus	100.0	854	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.92	96.44	0.98	0.96	4	conclusive
GCF_014253065.1	s__Campylobacter_A sp014253065	90.0015	616	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900699785.1	s__Campylobacter_A showae_D	89.8856	594	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900573985.1	s__Campylobacter_A showae_E	89.6767	628	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803815.1	s__Campylobacter_A showae	89.2042	591	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000344295.2	s__Campylobacter_A showae_B	89.0343	508	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372745.1	s__Campylobacter_A sp905372745	88.6294	538	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313615.1	s__Campylobacter_A showae_A	88.4946	569	857	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.64	96.14	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,639] [INFO] GTDB search result was written to GCF_004803795.1_ASM480379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:20,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:20,643] [INFO] DFAST_QC result json was written to GCF_004803795.1_ASM480379v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:20,643] [INFO] DFAST_QC completed!
[2024-01-24 11:13:20,643] [INFO] Total running time: 0h0m41s