[2023-06-28 06:10:12,853] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:10:12,857] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:10:12,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference
[2023-06-28 06:10:14,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:10:14,525] [INFO] Task started: Prodigal
[2023-06-28 06:10:14,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg8887d7d6-f50e-4f86-89a4-fa5574b7ee41/GCA_017472945.1_ASM1747294v1_genomic.fna.gz | prodigal -d GCA_017472945.1_ASM1747294v1_genomic.fna/cds.fna -a GCA_017472945.1_ASM1747294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:10:16,984] [INFO] Task succeeded: Prodigal
[2023-06-28 06:10:16,985] [INFO] Task started: HMMsearch
[2023-06-28 06:10:16,985] [INFO] Running command: hmmsearch --tblout GCA_017472945.1_ASM1747294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/reference_markers.hmm GCA_017472945.1_ASM1747294v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:10:17,185] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:10:17,188] [INFO] Found 6/6 markers.
[2023-06-28 06:10:17,215] [INFO] Query marker FASTA was written to GCA_017472945.1_ASM1747294v1_genomic.fna/markers.fasta
[2023-06-28 06:10:17,215] [INFO] Task started: Blastn
[2023-06-28 06:10:17,215] [INFO] Running command: blastn -query GCA_017472945.1_ASM1747294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/reference_markers.fasta -out GCA_017472945.1_ASM1747294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:18,477] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:18,482] [INFO] Selected 11 target genomes.
[2023-06-28 06:10:18,482] [INFO] Target genome list was writen to GCA_017472945.1_ASM1747294v1_genomic.fna/target_genomes.txt
[2023-06-28 06:10:18,483] [INFO] Task started: fastANI
[2023-06-28 06:10:18,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg8887d7d6-f50e-4f86-89a4-fa5574b7ee41/GCA_017472945.1_ASM1747294v1_genomic.fna.gz --refList GCA_017472945.1_ASM1747294v1_genomic.fna/target_genomes.txt --output GCA_017472945.1_ASM1747294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:10:22,278] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:22,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:10:22,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:10:22,288] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:10:22,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:10:22,288] [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 lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	83.2724	387	504	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	79.1529	151	504	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	79.0474	154	504	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	79.0229	159	504	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	78.2643	137	504	95	below_threshold
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	78.1065	137	504	95	below_threshold
Campylobacter fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	77.5956	145	504	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	77.5906	145	504	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	77.5548	146	504	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:10:22,290] [INFO] DFAST Taxonomy check result was written to GCA_017472945.1_ASM1747294v1_genomic.fna/tc_result.tsv
[2023-06-28 06:10:22,292] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:10:22,292] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:10:22,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/checkm_data
[2023-06-28 06:10:22,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:10:22,320] [INFO] Task started: CheckM
[2023-06-28 06:10:22,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017472945.1_ASM1747294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017472945.1_ASM1747294v1_genomic.fna/checkm_input GCA_017472945.1_ASM1747294v1_genomic.fna/checkm_result
[2023-06-28 06:10:39,491] [INFO] Task succeeded: CheckM
[2023-06-28 06:10:39,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:10:39,528] [INFO] ===== Completeness check finished =====
[2023-06-28 06:10:39,529] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:10:39,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017472945.1_ASM1747294v1_genomic.fna/markers.fasta)
[2023-06-28 06:10:39,530] [INFO] Task started: Blastn
[2023-06-28 06:10:39,530] [INFO] Running command: blastn -query GCA_017472945.1_ASM1747294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd8e298-05f9-4f2c-8caa-3de01afee612/dqc_reference/reference_markers_gtdb.fasta -out GCA_017472945.1_ASM1747294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:40,440] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:40,446] [INFO] Selected 6 target genomes.
[2023-06-28 06:10:40,446] [INFO] Target genome list was writen to GCA_017472945.1_ASM1747294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:10:40,451] [INFO] Task started: fastANI
[2023-06-28 06:10:40,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg8887d7d6-f50e-4f86-89a4-fa5574b7ee41/GCA_017472945.1_ASM1747294v1_genomic.fna.gz --refList GCA_017472945.1_ASM1747294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017472945.1_ASM1747294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:10:42,896] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:42,910] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:10:42,911] [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_002139875.1	s__Campylobacter sp002139875	97.5439	452	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.96	97.26	0.92	0.83	16	conclusive
GCA_017506845.1	s__Campylobacter sp017506845	92.6576	315	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.29	97.15	0.81	0.79	3	-
GCF_002139915.1	s__Campylobacter sp002139915	88.4597	414	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.90	97.72	0.92	0.90	37	-
GCA_017646085.1	s__Campylobacter sp017646085	88.3245	350	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002139855.1	s__Campylobacter sp002139855	83.4673	383	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_002139935.1	s__Campylobacter lanienae	83.2857	387	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.68	97.32	0.93	0.87	30	-
--------------------------------------------------------------------------------
[2023-06-28 06:10:42,914] [INFO] GTDB search result was written to GCA_017472945.1_ASM1747294v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:10:42,915] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:10:42,921] [INFO] DFAST_QC result json was written to GCA_017472945.1_ASM1747294v1_genomic.fna/dqc_result.json
[2023-06-28 06:10:42,921] [INFO] DFAST_QC completed!
[2023-06-28 06:10:42,921] [INFO] Total running time: 0h0m30s