[2024-01-24 12:40:07,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,205] [INFO] DQC Reference Directory: /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference
[2024-01-24 12:40:08,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,420] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgf593d5ec-6fc7-4746-a246-fabcfa4ea317/GCF_019930945.1_ASM1993094v1_genomic.fna.gz | prodigal -d GCF_019930945.1_ASM1993094v1_genomic.fna/cds.fna -a GCF_019930945.1_ASM1993094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:11,696] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:11,697] [INFO] Task started: HMMsearch
[2024-01-24 12:40:11,697] [INFO] Running command: hmmsearch --tblout GCF_019930945.1_ASM1993094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/reference_markers.hmm GCF_019930945.1_ASM1993094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:11,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:11,860] [INFO] Found 6/6 markers.
[2024-01-24 12:40:11,877] [INFO] Query marker FASTA was written to GCF_019930945.1_ASM1993094v1_genomic.fna/markers.fasta
[2024-01-24 12:40:11,877] [INFO] Task started: Blastn
[2024-01-24 12:40:11,877] [INFO] Running command: blastn -query GCF_019930945.1_ASM1993094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/reference_markers.fasta -out GCF_019930945.1_ASM1993094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:12,470] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:12,473] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:12,473] [INFO] Target genome list was writen to GCF_019930945.1_ASM1993094v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:12,479] [INFO] Task started: fastANI
[2024-01-24 12:40:12,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgf593d5ec-6fc7-4746-a246-fabcfa4ea317/GCF_019930945.1_ASM1993094v1_genomic.fna.gz --refList GCF_019930945.1_ASM1993094v1_genomic.fna/target_genomes.txt --output GCF_019930945.1_ASM1993094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:17,363] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:17,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:17,373] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:17,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:17,374] [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 hominis	strain=FDAARGOS_1467	GCA_019930945.1	76517	76517	type	True	100.0	570	571	95	conclusive
Campylobacter hominis	strain=NCTC13146	GCA_900446395.1	76517	76517	type	True	99.9994	569	571	95	conclusive
Campylobacter hominis	strain=ATCC BAA-381	GCA_000017585.1	76517	76517	type	True	99.9964	570	571	95	conclusive
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	77.2594	83	571	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	76.9782	65	571	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	76.7197	79	571	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	76.5703	63	571	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	76.0584	65	571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,375] [INFO] DFAST Taxonomy check result was written to GCF_019930945.1_ASM1993094v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:17,376] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:17,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:17,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/checkm_data
[2024-01-24 12:40:17,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:17,398] [INFO] Task started: CheckM
[2024-01-24 12:40:17,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930945.1_ASM1993094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930945.1_ASM1993094v1_genomic.fna/checkm_input GCF_019930945.1_ASM1993094v1_genomic.fna/checkm_result
[2024-01-24 12:40:33,987] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:33,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,004] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:34,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:34,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930945.1_ASM1993094v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:34,005] [INFO] Task started: Blastn
[2024-01-24 12:40:34,005] [INFO] Running command: blastn -query GCF_019930945.1_ASM1993094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87050a3-0daa-4f92-b021-ec2dfdce2e6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930945.1_ASM1993094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:34,813] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:34,817] [INFO] Selected 24 target genomes.
[2024-01-24 12:40:34,817] [INFO] Target genome list was writen to GCF_019930945.1_ASM1993094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:34,833] [INFO] Task started: fastANI
[2024-01-24 12:40:34,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgf593d5ec-6fc7-4746-a246-fabcfa4ea317/GCF_019930945.1_ASM1993094v1_genomic.fna.gz --refList GCF_019930945.1_ASM1993094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930945.1_ASM1993094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:41,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,978] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:41,978] [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_000017585.1	s__Campylobacter_B hominis	99.9964	570	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCA_000495505.1	s__Campylobacter testudinum	77.7183	58	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.40	99.13	0.96	0.89	37	-
GCA_017469645.1	s__Campylobacter_B sp017469645	77.296	106	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	95.68	95.54	0.84	0.81	3	-
GCF_900475935.1	s__Campylobacter fetus	76.9702	65	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCF_013201685.1	s__Campylobacter_B geochelonis	76.9403	82	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.40	99.12	0.97	0.95	4	-
GCF_001457695.1	s__Campylobacter_D jejuni	76.7992	67	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	76.6949	50	571	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_004378855.1	s__Campylobacter_D sp004378855	76.0331	64	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017934385.1	s__Campylobacter_B sp017934385	75.7463	54	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,980] [INFO] GTDB search result was written to GCF_019930945.1_ASM1993094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:41,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:41,983] [INFO] DFAST_QC result json was written to GCF_019930945.1_ASM1993094v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:41,984] [INFO] DFAST_QC completed!
[2024-01-24 12:40:41,984] [INFO] Total running time: 0h0m35s