[2024-01-25 19:54:35,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:35,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:35,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference
[2024-01-25 19:54:36,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:36,641] [INFO] Task started: Prodigal
[2024-01-25 19:54:36,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg793a7e0e-2abd-418b-96eb-2f0c0f0eceba/GCF_016766895.1_ASM1676689v1_genomic.fna.gz | prodigal -d GCF_016766895.1_ASM1676689v1_genomic.fna/cds.fna -a GCF_016766895.1_ASM1676689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:39,346] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:39,347] [INFO] Task started: HMMsearch
[2024-01-25 19:54:39,347] [INFO] Running command: hmmsearch --tblout GCF_016766895.1_ASM1676689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/reference_markers.hmm GCF_016766895.1_ASM1676689v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:39,515] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:39,516] [INFO] Found 6/6 markers.
[2024-01-25 19:54:39,534] [INFO] Query marker FASTA was written to GCF_016766895.1_ASM1676689v1_genomic.fna/markers.fasta
[2024-01-25 19:54:39,534] [INFO] Task started: Blastn
[2024-01-25 19:54:39,534] [INFO] Running command: blastn -query GCF_016766895.1_ASM1676689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/reference_markers.fasta -out GCF_016766895.1_ASM1676689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:40,068] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:40,070] [INFO] Selected 7 target genomes.
[2024-01-25 19:54:40,071] [INFO] Target genome list was writen to GCF_016766895.1_ASM1676689v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:40,079] [INFO] Task started: fastANI
[2024-01-25 19:54:40,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg793a7e0e-2abd-418b-96eb-2f0c0f0eceba/GCF_016766895.1_ASM1676689v1_genomic.fna.gz --refList GCF_016766895.1_ASM1676689v1_genomic.fna/target_genomes.txt --output GCF_016766895.1_ASM1676689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:43,203] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:43,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:43,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:43,210] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:54:43,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:43,210] [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 ureolyticus	strain=FDAARGOS_1102	GCA_016766895.1	827	827	suspected-type	True	100.0	602	608	95	conclusive
Campylobacter ureolyticus	strain=LMG 6451	GCA_013372225.1	827	827	suspected-type	True	99.9986	598	608	95	conclusive
Campylobacter ureolyticus	strain=NCTC10941	GCA_900460885.1	827	827	suspected-type	True	99.9985	600	608	95	conclusive
Campylobacter ureolyticus	strain=DSM 20703	GCA_000374605.1	827	827	suspected-type	True	99.9594	561	608	95	conclusive
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	78.1612	230	608	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	77.817	233	608	95	below_threshold
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	77.7919	203	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:43,211] [INFO] DFAST Taxonomy check result was written to GCF_016766895.1_ASM1676689v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:43,212] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:43,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:43,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/checkm_data
[2024-01-25 19:54:43,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:43,234] [INFO] Task started: CheckM
[2024-01-25 19:54:43,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016766895.1_ASM1676689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016766895.1_ASM1676689v1_genomic.fna/checkm_input GCF_016766895.1_ASM1676689v1_genomic.fna/checkm_result
[2024-01-25 19:54:57,699] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:57,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:57,713] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:57,714] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:57,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016766895.1_ASM1676689v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:57,714] [INFO] Task started: Blastn
[2024-01-25 19:54:57,714] [INFO] Running command: blastn -query GCF_016766895.1_ASM1676689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39b1f195-ecdb-4f8d-afcb-689a8f55018d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016766895.1_ASM1676689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:58,460] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:58,463] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:58,463] [INFO] Target genome list was writen to GCF_016766895.1_ASM1676689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:58,469] [INFO] Task started: fastANI
[2024-01-25 19:54:58,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg793a7e0e-2abd-418b-96eb-2f0c0f0eceba/GCF_016766895.1_ASM1676689v1_genomic.fna.gz --refList GCF_016766895.1_ASM1676689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016766895.1_ASM1676689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:02,417] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:02,427] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:02,427] [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_013372225.1	s__Campylobacter_B ureolyticus	99.9986	598	608	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	97.14	95.63	0.91	0.85	10	conclusive
GCF_000413435.1	s__Campylobacter_B ureolyticus_A	94.8776	455	608	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_013201645.1	s__Campylobacter_B corcagiensis	78.1836	231	608	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_009690845.1	s__Campylobacter_B portucalensis	77.8153	233	608	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_013201895.1	s__Campylobacter_B blaseri	77.6209	201	608	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	77.6109	187	608	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_008245005.1	s__Campylobacter_B sputorum	77.5974	152	608	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.49	98.05	0.98	0.93	7	-
GCF_002220775.1	s__Campylobacter_B sputorum_B	77.326	152	608	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.55	97.99	0.98	0.90	7	-
GCA_000495505.1	s__Campylobacter testudinum	76.8309	91	608	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.40	99.13	0.96	0.89	37	-
GCA_012728225.1	s__Campylobacter_B sp012728225	76.7758	107	608	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_017934385.1	s__Campylobacter_B sp017934385	75.5624	50	608	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:02,428] [INFO] GTDB search result was written to GCF_016766895.1_ASM1676689v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:02,429] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:02,432] [INFO] DFAST_QC result json was written to GCF_016766895.1_ASM1676689v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:02,432] [INFO] DFAST_QC completed!
[2024-01-25 19:55:02,432] [INFO] Total running time: 0h0m27s