[2024-01-24 14:12:15,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:15,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:15,818] [INFO] DQC Reference Directory: /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference
[2024-01-24 14:12:17,328] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:17,329] [INFO] Task started: Prodigal
[2024-01-24 14:12:17,329] [INFO] Running command: gunzip -c /var/lib/cwl/stgea081b10-3d63-444d-b341-d4d9ad9a4158/GCF_030249945.1_ASM3024994v1_genomic.fna.gz | prodigal -d GCF_030249945.1_ASM3024994v1_genomic.fna/cds.fna -a GCF_030249945.1_ASM3024994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:20,471] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:20,472] [INFO] Task started: HMMsearch
[2024-01-24 14:12:20,472] [INFO] Running command: hmmsearch --tblout GCF_030249945.1_ASM3024994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/reference_markers.hmm GCF_030249945.1_ASM3024994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:20,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:20,737] [INFO] Found 6/6 markers.
[2024-01-24 14:12:20,759] [INFO] Query marker FASTA was written to GCF_030249945.1_ASM3024994v1_genomic.fna/markers.fasta
[2024-01-24 14:12:20,759] [INFO] Task started: Blastn
[2024-01-24 14:12:20,760] [INFO] Running command: blastn -query GCF_030249945.1_ASM3024994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/reference_markers.fasta -out GCF_030249945.1_ASM3024994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:21,437] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:21,443] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:21,444] [INFO] Target genome list was writen to GCF_030249945.1_ASM3024994v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:21,496] [INFO] Task started: fastANI
[2024-01-24 14:12:21,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgea081b10-3d63-444d-b341-d4d9ad9a4158/GCF_030249945.1_ASM3024994v1_genomic.fna.gz --refList GCF_030249945.1_ASM3024994v1_genomic.fna/target_genomes.txt --output GCF_030249945.1_ASM3024994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:25,714] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:25,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:25,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:25,730] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:25,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:25,730] [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	83.2456	412	523	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	79.0992	178	523	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	78.9702	172	523	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	78.9182	166	523	95	below_threshold
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	78.1227	151	523	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	77.6827	150	523	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	77.621	152	523	95	below_threshold
Campylobacter fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	77.6082	154	523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:25,732] [INFO] DFAST Taxonomy check result was written to GCF_030249945.1_ASM3024994v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:25,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:25,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:25,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/checkm_data
[2024-01-24 14:12:25,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:25,755] [INFO] Task started: CheckM
[2024-01-24 14:12:25,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030249945.1_ASM3024994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030249945.1_ASM3024994v1_genomic.fna/checkm_input GCF_030249945.1_ASM3024994v1_genomic.fna/checkm_result
[2024-01-24 14:12:42,952] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:42,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:42,976] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:42,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:42,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030249945.1_ASM3024994v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:42,978] [INFO] Task started: Blastn
[2024-01-24 14:12:42,978] [INFO] Running command: blastn -query GCF_030249945.1_ASM3024994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga122a5fb-f868-4075-9683-f7e8afde1dca/dqc_reference/reference_markers_gtdb.fasta -out GCF_030249945.1_ASM3024994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:43,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:43,783] [INFO] Selected 6 target genomes.
[2024-01-24 14:12:43,784] [INFO] Target genome list was writen to GCF_030249945.1_ASM3024994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:43,789] [INFO] Task started: fastANI
[2024-01-24 14:12:43,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgea081b10-3d63-444d-b341-d4d9ad9a4158/GCF_030249945.1_ASM3024994v1_genomic.fna.gz --refList GCF_030249945.1_ASM3024994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030249945.1_ASM3024994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:46,105] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:46,115] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:46,115] [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	97.4427	488	523	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	92.2845	321	523	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	88.3991	431	523	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	88.3166	347	523	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	83.5783	416	523	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	83.2456	412	523	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.68	97.32	0.93	0.87	30	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:46,117] [INFO] GTDB search result was written to GCF_030249945.1_ASM3024994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:46,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:46,120] [INFO] DFAST_QC result json was written to GCF_030249945.1_ASM3024994v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:46,121] [INFO] DFAST_QC completed!
[2024-01-24 14:12:46,121] [INFO] Total running time: 0h0m30s