[2024-01-24 13:19:29,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:29,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:29,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference
[2024-01-24 13:19:30,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:30,381] [INFO] Task started: Prodigal
[2024-01-24 13:19:30,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f443968-b0de-4bdc-879e-919440d28f47/GCF_013201895.1_ASM1320189v1_genomic.fna.gz | prodigal -d GCF_013201895.1_ASM1320189v1_genomic.fna/cds.fna -a GCF_013201895.1_ASM1320189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:33,759] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:33,760] [INFO] Task started: HMMsearch
[2024-01-24 13:19:33,760] [INFO] Running command: hmmsearch --tblout GCF_013201895.1_ASM1320189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/reference_markers.hmm GCF_013201895.1_ASM1320189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:34,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:34,036] [INFO] Found 6/6 markers.
[2024-01-24 13:19:34,064] [INFO] Query marker FASTA was written to GCF_013201895.1_ASM1320189v1_genomic.fna/markers.fasta
[2024-01-24 13:19:34,065] [INFO] Task started: Blastn
[2024-01-24 13:19:34,065] [INFO] Running command: blastn -query GCF_013201895.1_ASM1320189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/reference_markers.fasta -out GCF_013201895.1_ASM1320189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,682] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:34,682] [INFO] Target genome list was writen to GCF_013201895.1_ASM1320189v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:34,694] [INFO] Task started: fastANI
[2024-01-24 13:19:34,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f443968-b0de-4bdc-879e-919440d28f47/GCF_013201895.1_ASM1320189v1_genomic.fna.gz --refList GCF_013201895.1_ASM1320189v1_genomic.fna/target_genomes.txt --output GCF_013201895.1_ASM1320189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:38,175] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:38,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:38,186] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:38,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:38,187] [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=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	100.0	627	630	95	conclusive
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	99.9777	612	630	95	conclusive
Campylobacter ureolyticus	strain=FDAARGOS_1102	GCA_016766895.1	827	827	suspected-type	True	77.6334	206	630	95	below_threshold
Campylobacter ureolyticus	strain=NCTC10941	GCA_900460885.1	827	827	suspected-type	True	77.6261	202	630	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	77.5682	168	630	95	below_threshold
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	77.5679	170	630	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	77.2692	166	630	95	below_threshold
Campylobacter corcagiensis	strain=CIT 045	GCA_000597805.1	1448857	1448857	type	True	77.242	165	630	95	below_threshold
Campylobacter ureolyticus	strain=DSM 20703	GCA_000374605.1	827	827	suspected-type	True	77.2396	198	630	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	77.1445	182	630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:38,189] [INFO] DFAST Taxonomy check result was written to GCF_013201895.1_ASM1320189v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:38,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:38,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:38,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/checkm_data
[2024-01-24 13:19:38,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:38,213] [INFO] Task started: CheckM
[2024-01-24 13:19:38,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201895.1_ASM1320189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201895.1_ASM1320189v1_genomic.fna/checkm_input GCF_013201895.1_ASM1320189v1_genomic.fna/checkm_result
[2024-01-24 13:19:55,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:55,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:55,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:55,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201895.1_ASM1320189v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:55,872] [INFO] Task started: Blastn
[2024-01-24 13:19:55,872] [INFO] Running command: blastn -query GCF_013201895.1_ASM1320189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2612cab1-527b-4f0c-9a17-aee76b983d92/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201895.1_ASM1320189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:56,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:56,672] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:56,672] [INFO] Target genome list was writen to GCF_013201895.1_ASM1320189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:56,682] [INFO] Task started: fastANI
[2024-01-24 13:19:56,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f443968-b0de-4bdc-879e-919440d28f47/GCF_013201895.1_ASM1320189v1_genomic.fna.gz --refList GCF_013201895.1_ASM1320189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201895.1_ASM1320189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:00,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:00,521] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:00,522] [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	100.0	628	630	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	78.8462	137	630	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_013372225.1	s__Campylobacter_B ureolyticus	77.5952	206	630	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_000413435.1	s__Campylobacter_B ureolyticus_A	77.5879	197	630	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_013201685.1	s__Campylobacter_B geochelonis	77.5497	169	630	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_013201645.1	s__Campylobacter_B corcagiensis	77.4581	170	630	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_900475935.1	s__Campylobacter fetus	77.3305	81	630	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCF_008245005.1	s__Campylobacter_B sputorum	77.2072	142	630	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_009690845.1	s__Campylobacter_B portucalensis	77.1599	181	630	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_013372105.1	s__Campylobacter_D armoricus	76.8401	92	630	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	-
GCA_012728225.1	s__Campylobacter_B sp012728225	76.0318	102	630	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 13:20:00,523] [INFO] GTDB search result was written to GCF_013201895.1_ASM1320189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:00,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:00,527] [INFO] DFAST_QC result json was written to GCF_013201895.1_ASM1320189v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:00,527] [INFO] DFAST_QC completed!
[2024-01-24 13:20:00,527] [INFO] Total running time: 0h0m32s