[2024-01-24 13:19:01,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,477] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,477] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference
[2024-01-24 13:19:02,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,893] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b01d6f8-161b-4847-a6dd-6ff81cafff2f/GCF_009690845.1_ASM969084v1_genomic.fna.gz | prodigal -d GCF_009690845.1_ASM969084v1_genomic.fna/cds.fna -a GCF_009690845.1_ASM969084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:05,577] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:05,578] [INFO] Task started: HMMsearch
[2024-01-24 13:19:05,578] [INFO] Running command: hmmsearch --tblout GCF_009690845.1_ASM969084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/reference_markers.hmm GCF_009690845.1_ASM969084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:05,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:05,786] [INFO] Found 6/6 markers.
[2024-01-24 13:19:05,807] [INFO] Query marker FASTA was written to GCF_009690845.1_ASM969084v1_genomic.fna/markers.fasta
[2024-01-24 13:19:05,807] [INFO] Task started: Blastn
[2024-01-24 13:19:05,807] [INFO] Running command: blastn -query GCF_009690845.1_ASM969084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/reference_markers.fasta -out GCF_009690845.1_ASM969084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:06,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:06,426] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:06,427] [INFO] Target genome list was writen to GCF_009690845.1_ASM969084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:06,438] [INFO] Task started: fastANI
[2024-01-24 13:19:06,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b01d6f8-161b-4847-a6dd-6ff81cafff2f/GCF_009690845.1_ASM969084v1_genomic.fna.gz --refList GCF_009690845.1_ASM969084v1_genomic.fna/target_genomes.txt --output GCF_009690845.1_ASM969084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:09,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:09,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:09,572] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:09,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:09,572] [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 portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	100.0	549	551	95	conclusive
Campylobacter ureolyticus	strain=NCTC10941	GCA_900460885.1	827	827	suspected-type	True	78.1144	225	551	95	below_threshold
Campylobacter ureolyticus	strain=LMG 6451	GCA_013372225.1	827	827	suspected-type	True	78.0818	225	551	95	below_threshold
Campylobacter ureolyticus	strain=FDAARGOS_1102	GCA_016766895.1	827	827	suspected-type	True	78.0517	230	551	95	below_threshold
Campylobacter ureolyticus	strain=DSM 20703	GCA_000374605.1	827	827	suspected-type	True	78.0192	223	551	95	below_threshold
Campylobacter corcagiensis	strain=CIT 045	GCA_000597805.1	1448857	1448857	type	True	77.8853	181	551	95	below_threshold
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	77.836	183	551	95	below_threshold
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	77.1586	178	551	95	below_threshold
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	77.1578	175	551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:09,573] [INFO] DFAST Taxonomy check result was written to GCF_009690845.1_ASM969084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:09,574] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:09,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:09,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/checkm_data
[2024-01-24 13:19:09,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:09,596] [INFO] Task started: CheckM
[2024-01-24 13:19:09,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009690845.1_ASM969084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009690845.1_ASM969084v1_genomic.fna/checkm_input GCF_009690845.1_ASM969084v1_genomic.fna/checkm_result
[2024-01-24 13:19:27,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:27,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:27,489] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:27,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:27,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009690845.1_ASM969084v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:27,490] [INFO] Task started: Blastn
[2024-01-24 13:19:27,490] [INFO] Running command: blastn -query GCF_009690845.1_ASM969084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f086b5-dda5-41e1-8203-2873f0be4e42/dqc_reference/reference_markers_gtdb.fasta -out GCF_009690845.1_ASM969084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:28,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:28,292] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:28,292] [INFO] Target genome list was writen to GCF_009690845.1_ASM969084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:28,307] [INFO] Task started: fastANI
[2024-01-24 13:19:28,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b01d6f8-161b-4847-a6dd-6ff81cafff2f/GCF_009690845.1_ASM969084v1_genomic.fna.gz --refList GCF_009690845.1_ASM969084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009690845.1_ASM969084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:33,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:33,011] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:33,012] [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_009690845.1	s__Campylobacter_B portucalensis	100.0	549	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013372225.1	s__Campylobacter_B ureolyticus	78.131	222	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	97.14	95.63	0.91	0.85	10	-
GCF_013201645.1	s__Campylobacter_B corcagiensis	77.8549	182	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000413435.1	s__Campylobacter_B ureolyticus_A	77.7336	227	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220775.1	s__Campylobacter_B sputorum_B	77.3065	151	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.55	97.99	0.98	0.90	7	-
GCF_013201895.1	s__Campylobacter_B blaseri	77.1734	174	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_012519705.1	s__Campylobacter_B sp012519705	77.0322	131	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728225.1	s__Campylobacter_B sp012728225	76.7595	108	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008245045.1	s__Campylobacter_D volucris	76.3099	88	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	97.46	0.95	0.86	15	-
GCF_013372185.1	s__Campylobacter_D lari	76.2327	86	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.73	98.09	0.96	0.93	13	-
GCF_013372105.1	s__Campylobacter_D armoricus	76.2107	87	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	-
GCF_008011665.1	s__Campylobacter_D volucris_A	75.9613	99	551	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,013] [INFO] GTDB search result was written to GCF_009690845.1_ASM969084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:33,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:33,017] [INFO] DFAST_QC result json was written to GCF_009690845.1_ASM969084v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:33,018] [INFO] DFAST_QC completed!
[2024-01-24 13:19:33,018] [INFO] Total running time: 0h0m32s