[2024-01-24 13:33:41,148] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference
[2024-01-24 13:33:42,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,401] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b5ff39c-2371-473a-a8cd-1665e3b21c6b/GCF_000017585.1_ASM1758v1_genomic.fna.gz | prodigal -d GCF_000017585.1_ASM1758v1_genomic.fna/cds.fna -a GCF_000017585.1_ASM1758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:45,626] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:45,626] [INFO] Task started: HMMsearch
[2024-01-24 13:33:45,626] [INFO] Running command: hmmsearch --tblout GCF_000017585.1_ASM1758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/reference_markers.hmm GCF_000017585.1_ASM1758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:45,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:45,832] [INFO] Found 6/6 markers.
[2024-01-24 13:33:45,855] [INFO] Query marker FASTA was written to GCF_000017585.1_ASM1758v1_genomic.fna/markers.fasta
[2024-01-24 13:33:45,856] [INFO] Task started: Blastn
[2024-01-24 13:33:45,856] [INFO] Running command: blastn -query GCF_000017585.1_ASM1758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/reference_markers.fasta -out GCF_000017585.1_ASM1758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:46,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:46,435] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:46,436] [INFO] Target genome list was writen to GCF_000017585.1_ASM1758v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:46,666] [INFO] Task started: fastANI
[2024-01-24 13:33:46,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5ff39c-2371-473a-a8cd-1665e3b21c6b/GCF_000017585.1_ASM1758v1_genomic.fna.gz --refList GCF_000017585.1_ASM1758v1_genomic.fna/target_genomes.txt --output GCF_000017585.1_ASM1758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:51,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:51,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:51,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:52,008] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:52,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:52,008] [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=ATCC BAA-381	GCA_000017585.1	76517	76517	type	True	100.0	569	571	95	conclusive
Campylobacter hominis	strain=NCTC13146	GCA_900446395.1	76517	76517	type	True	99.9994	569	571	95	conclusive
Campylobacter hominis	strain=FDAARGOS_1467	GCA_019930945.1	76517	76517	type	True	99.9964	569	571	95	conclusive
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	77.0977	58	571	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	76.7381	89	571	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	76.5443	84	571	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	76.5214	57	571	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	76.1029	63	571	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	75.9216	57	571	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	74.7823	52	571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,010] [INFO] DFAST Taxonomy check result was written to GCF_000017585.1_ASM1758v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:52,011] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:52,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:52,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/checkm_data
[2024-01-24 13:33:52,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:52,040] [INFO] Task started: CheckM
[2024-01-24 13:33:52,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017585.1_ASM1758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017585.1_ASM1758v1_genomic.fna/checkm_input GCF_000017585.1_ASM1758v1_genomic.fna/checkm_result
[2024-01-24 13:34:09,203] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:09,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,224] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:09,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:09,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017585.1_ASM1758v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:09,225] [INFO] Task started: Blastn
[2024-01-24 13:34:09,225] [INFO] Running command: blastn -query GCF_000017585.1_ASM1758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5635ba-0666-4a14-80a9-e5b64a3f68a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017585.1_ASM1758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:10,037] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:10,041] [INFO] Selected 24 target genomes.
[2024-01-24 13:34:10,041] [INFO] Target genome list was writen to GCF_000017585.1_ASM1758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:10,577] [INFO] Task started: fastANI
[2024-01-24 13:34:10,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5ff39c-2371-473a-a8cd-1665e3b21c6b/GCF_000017585.1_ASM1758v1_genomic.fna.gz --refList GCF_000017585.1_ASM1758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017585.1_ASM1758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:17,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:17,778] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:17,778] [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	100.0	568	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	77.7026	51	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	77.2018	111	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	77.095	58	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	76.8858	90	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	76.7475	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	76.7415	51	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_002179165.1	s__Campylobacter_D jejuni_B	76.4424	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_003346775.1	s__Malaciobacter mytili	76.3677	59	571	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_008011665.1	s__Campylobacter_D volucris_A	76.1454	53	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	76.0391	51	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	-
GCF_004378855.1	s__Campylobacter_D sp004378855	75.9544	66	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:17,780] [INFO] GTDB search result was written to GCF_000017585.1_ASM1758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:17,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:17,784] [INFO] DFAST_QC result json was written to GCF_000017585.1_ASM1758v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:17,784] [INFO] DFAST_QC completed!
[2024-01-24 13:34:17,784] [INFO] Total running time: 0h0m37s