[2024-01-24 12:42:09,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference
[2024-01-24 12:42:10,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,581] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,582] [INFO] Running command: gunzip -c /var/lib/cwl/stga44b5d4b-649e-4b12-bd5d-70657baadaf6/GCF_016806695.1_ASM1680669v1_genomic.fna.gz | prodigal -d GCF_016806695.1_ASM1680669v1_genomic.fna/cds.fna -a GCF_016806695.1_ASM1680669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:13,060] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:13,060] [INFO] Task started: HMMsearch
[2024-01-24 12:42:13,061] [INFO] Running command: hmmsearch --tblout GCF_016806695.1_ASM1680669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/reference_markers.hmm GCF_016806695.1_ASM1680669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:13,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:13,317] [INFO] Found 6/6 markers.
[2024-01-24 12:42:13,340] [INFO] Query marker FASTA was written to GCF_016806695.1_ASM1680669v1_genomic.fna/markers.fasta
[2024-01-24 12:42:13,341] [INFO] Task started: Blastn
[2024-01-24 12:42:13,341] [INFO] Running command: blastn -query GCF_016806695.1_ASM1680669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/reference_markers.fasta -out GCF_016806695.1_ASM1680669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:13,930] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:13,935] [INFO] Selected 10 target genomes.
[2024-01-24 12:42:13,936] [INFO] Target genome list was writen to GCF_016806695.1_ASM1680669v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:13,960] [INFO] Task started: fastANI
[2024-01-24 12:42:13,960] [INFO] Running command: fastANI --query /var/lib/cwl/stga44b5d4b-649e-4b12-bd5d-70657baadaf6/GCF_016806695.1_ASM1680669v1_genomic.fna.gz --refList GCF_016806695.1_ASM1680669v1_genomic.fna/target_genomes.txt --output GCF_016806695.1_ASM1680669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:17,057] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:17,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:17,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:17,068] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:17,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:17,068] [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 bilis	strain=VicNov18	GCA_016806695.1	2691918	2691918	type	True	100.0	460	464	95	conclusive
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	85.2693	423	464	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	83.9465	361	464	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=type strain: CCUG11284	GCA_905410075.1	32022	197	type	True	83.7849	398	464	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	83.7266	403	464	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	83.7227	403	464	95	below_threshold
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	77.9803	201	464	95	below_threshold
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	77.8685	179	464	95	below_threshold
Campylobacter upsaliensis	strain=NCTC11541	GCA_900637395.1	28080	28080	type	True	77.8151	182	464	95	below_threshold
Campylobacter upsaliensis	strain=DSM 5365	GCA_000620965.1	28080	28080	type	True	77.5141	183	464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:17,070] [INFO] DFAST Taxonomy check result was written to GCF_016806695.1_ASM1680669v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:17,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:17,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:17,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/checkm_data
[2024-01-24 12:42:17,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:17,089] [INFO] Task started: CheckM
[2024-01-24 12:42:17,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016806695.1_ASM1680669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016806695.1_ASM1680669v1_genomic.fna/checkm_input GCF_016806695.1_ASM1680669v1_genomic.fna/checkm_result
[2024-01-24 12:42:32,599] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:32,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:32,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:32,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:32,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016806695.1_ASM1680669v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:32,621] [INFO] Task started: Blastn
[2024-01-24 12:42:32,621] [INFO] Running command: blastn -query GCF_016806695.1_ASM1680669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14df938e-93c7-4028-bffe-36f42a51ee41/dqc_reference/reference_markers_gtdb.fasta -out GCF_016806695.1_ASM1680669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:33,413] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:33,417] [INFO] Selected 11 target genomes.
[2024-01-24 12:42:33,417] [INFO] Target genome list was writen to GCF_016806695.1_ASM1680669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:33,426] [INFO] Task started: fastANI
[2024-01-24 12:42:33,426] [INFO] Running command: fastANI --query /var/lib/cwl/stga44b5d4b-649e-4b12-bd5d-70657baadaf6/GCF_016806695.1_ASM1680669v1_genomic.fna.gz --refList GCF_016806695.1_ASM1680669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016806695.1_ASM1680669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:37,150] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:37,160] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:37,160] [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_009362725.1	s__Campylobacter_D hepaticus_A	100.0	460	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_001687475.2	s__Campylobacter_D hepaticus	85.2693	423	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.94	99.56	0.99	0.97	33	-
GCF_001457695.1	s__Campylobacter_D jejuni	83.7227	403	464	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	83.6432	383	464	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_014305285.1	s__Campylobacter_D jejuni_D	83.5671	388	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	81.1287	338	464	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_016599045.1	s__Campylobacter_D sp016599045	79.1666	256	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.00	98.98	0.95	0.93	3	-
GCF_008245025.1	s__Campylobacter_D concheus	77.9803	201	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.27	98.88	0.96	0.94	4	-
GCF_900637395.1	s__Campylobacter_D upsaliensis	77.8697	179	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	96.80	95.96	0.91	0.88	18	-
GCF_002238335.1	s__Campylobacter_D avium	76.841	91	464	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:37,162] [INFO] GTDB search result was written to GCF_016806695.1_ASM1680669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:37,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:37,165] [INFO] DFAST_QC result json was written to GCF_016806695.1_ASM1680669v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:37,166] [INFO] DFAST_QC completed!
[2024-01-24 12:42:37,166] [INFO] Total running time: 0h0m28s