[2024-01-24 15:27:41,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference
[2024-01-24 15:27:43,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,886] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,886] [INFO] Running command: gunzip -c /var/lib/cwl/stge711ebd5-1675-44e5-8bc9-578e0fcbd198/GCF_003015205.1_ASM301520v1_genomic.fna.gz | prodigal -d GCF_003015205.1_ASM301520v1_genomic.fna/cds.fna -a GCF_003015205.1_ASM301520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:46,931] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:46,932] [INFO] Task started: HMMsearch
[2024-01-24 15:27:46,932] [INFO] Running command: hmmsearch --tblout GCF_003015205.1_ASM301520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/reference_markers.hmm GCF_003015205.1_ASM301520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:47,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:47,256] [INFO] Found 6/6 markers.
[2024-01-24 15:27:47,279] [INFO] Query marker FASTA was written to GCF_003015205.1_ASM301520v1_genomic.fna/markers.fasta
[2024-01-24 15:27:47,281] [INFO] Task started: Blastn
[2024-01-24 15:27:47,281] [INFO] Running command: blastn -query GCF_003015205.1_ASM301520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/reference_markers.fasta -out GCF_003015205.1_ASM301520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:50,970] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:50,976] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:50,976] [INFO] Target genome list was writen to GCF_003015205.1_ASM301520v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:51,081] [INFO] Task started: fastANI
[2024-01-24 15:27:51,082] [INFO] Running command: fastANI --query /var/lib/cwl/stge711ebd5-1675-44e5-8bc9-578e0fcbd198/GCF_003015205.1_ASM301520v1_genomic.fna.gz --refList GCF_003015205.1_ASM301520v1_genomic.fna/target_genomes.txt --output GCF_003015205.1_ASM301520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:54,528] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:54,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:54,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:54,546] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:54,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:54,546] [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 blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	100.0	613	614	95	conclusive
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	99.9975	613	614	95	conclusive
Campylobacter corcagiensis	strain=CIT 045	GCA_000597805.1	1448857	1448857	type	True	77.4549	159	614	95	below_threshold
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	77.4478	160	614	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	77.3838	172	614	95	below_threshold
Campylobacter ureolyticus	strain=FDAARGOS_1102	GCA_016766895.1	827	827	suspected-type	True	77.3666	189	614	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	77.349	160	614	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	77.3188	163	614	95	below_threshold
Campylobacter ureolyticus	strain=NCTC10941	GCA_900460885.1	827	827	suspected-type	True	77.2974	196	614	95	below_threshold
Campylobacter ureolyticus	strain=DSM 20703	GCA_000374605.1	827	827	suspected-type	True	77.2624	188	614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:54,548] [INFO] DFAST Taxonomy check result was written to GCF_003015205.1_ASM301520v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:54,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:54,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:54,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/checkm_data
[2024-01-24 15:27:54,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:54,574] [INFO] Task started: CheckM
[2024-01-24 15:27:54,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003015205.1_ASM301520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003015205.1_ASM301520v1_genomic.fna/checkm_input GCF_003015205.1_ASM301520v1_genomic.fna/checkm_result
[2024-01-24 15:28:15,683] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:15,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:15,703] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:15,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:15,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003015205.1_ASM301520v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:15,705] [INFO] Task started: Blastn
[2024-01-24 15:28:15,705] [INFO] Running command: blastn -query GCF_003015205.1_ASM301520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d720c91-975d-45d8-8adc-c11db5c29282/dqc_reference/reference_markers_gtdb.fasta -out GCF_003015205.1_ASM301520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:16,956] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:16,960] [INFO] Selected 12 target genomes.
[2024-01-24 15:28:16,960] [INFO] Target genome list was writen to GCF_003015205.1_ASM301520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:16,975] [INFO] Task started: fastANI
[2024-01-24 15:28:16,975] [INFO] Running command: fastANI --query /var/lib/cwl/stge711ebd5-1675-44e5-8bc9-578e0fcbd198/GCF_003015205.1_ASM301520v1_genomic.fna.gz --refList GCF_003015205.1_ASM301520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003015205.1_ASM301520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:21,115] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:21,124] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:21,125] [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_013201895.1	s__Campylobacter_B blaseri	99.9975	613	614	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
GCF_002021925.1	s__Campylobacter_A pinnipediorum	78.8735	118	614	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	-
GCF_000413435.1	s__Campylobacter_B ureolyticus_A	77.7131	180	614	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	77.4849	158	614	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_013201685.1	s__Campylobacter_B geochelonis	77.367	159	614	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_009690845.1	s__Campylobacter_B portucalensis	77.3658	173	614	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_013372225.1	s__Campylobacter_B ureolyticus	77.306	194	614	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	97.14	95.63	0.91	0.85	10	-
GCF_008245005.1	s__Campylobacter_B sputorum	77.0829	135	614	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_013372105.1	s__Campylobacter_D armoricus	76.8256	79	614	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	-
GCF_900475935.1	s__Campylobacter fetus	76.6471	75	614	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCA_012728225.1	s__Campylobacter_B sp012728225	76.469	88	614	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 15:28:21,126] [INFO] GTDB search result was written to GCF_003015205.1_ASM301520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:21,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:21,130] [INFO] DFAST_QC result json was written to GCF_003015205.1_ASM301520v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:21,130] [INFO] DFAST_QC completed!
[2024-01-24 15:28:21,130] [INFO] Total running time: 0h0m40s