[2024-01-24 14:30:47,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference
[2024-01-24 14:30:48,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,473] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf0bbce6-6820-4797-a9a4-e7bc518bf99c/GCF_905410075.1_ASM90541007v1_genomic.fna.gz | prodigal -d GCF_905410075.1_ASM90541007v1_genomic.fna/cds.fna -a GCF_905410075.1_ASM90541007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:51,414] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:51,414] [INFO] Task started: HMMsearch
[2024-01-24 14:30:51,415] [INFO] Running command: hmmsearch --tblout GCF_905410075.1_ASM90541007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/reference_markers.hmm GCF_905410075.1_ASM90541007v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:51,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:51,636] [INFO] Found 6/6 markers.
[2024-01-24 14:30:51,658] [INFO] Query marker FASTA was written to GCF_905410075.1_ASM90541007v1_genomic.fna/markers.fasta
[2024-01-24 14:30:51,658] [INFO] Task started: Blastn
[2024-01-24 14:30:51,658] [INFO] Running command: blastn -query GCF_905410075.1_ASM90541007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/reference_markers.fasta -out GCF_905410075.1_ASM90541007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:52,224] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:52,227] [INFO] Selected 5 target genomes.
[2024-01-24 14:30:52,227] [INFO] Target genome list was writen to GCF_905410075.1_ASM90541007v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:52,233] [INFO] Task started: fastANI
[2024-01-24 14:30:52,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0bbce6-6820-4797-a9a4-e7bc518bf99c/GCF_905410075.1_ASM90541007v1_genomic.fna.gz --refList GCF_905410075.1_ASM90541007v1_genomic.fna/target_genomes.txt --output GCF_905410075.1_ASM90541007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:54,262] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:54,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:54,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:54,268] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:30:54,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:54,268] [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 jejuni subsp. jejuni	strain=type strain: CCUG11284	GCA_905410075.1	32022	197	type	True	100.0	552	553	95	conclusive
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_003999645.1	32022	197	type	True	99.9991	553	553	95	conclusive
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	99.9981	552	553	95	conclusive
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	99.9965	551	553	95	conclusive
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	99.8825	476	553	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:30:54,270] [INFO] DFAST Taxonomy check result was written to GCF_905410075.1_ASM90541007v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:54,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:54,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:54,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/checkm_data
[2024-01-24 14:30:54,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:54,295] [INFO] Task started: CheckM
[2024-01-24 14:30:54,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905410075.1_ASM90541007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905410075.1_ASM90541007v1_genomic.fna/checkm_input GCF_905410075.1_ASM90541007v1_genomic.fna/checkm_result
[2024-01-24 14:31:11,273] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:11,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:11,293] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:11,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:11,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905410075.1_ASM90541007v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:11,294] [INFO] Task started: Blastn
[2024-01-24 14:31:11,294] [INFO] Running command: blastn -query GCF_905410075.1_ASM90541007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366b2ccb-2aa0-4862-aa4e-ab380885c3a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_905410075.1_ASM90541007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:12,172] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:12,177] [INFO] Selected 8 target genomes.
[2024-01-24 14:31:12,177] [INFO] Target genome list was writen to GCF_905410075.1_ASM90541007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:12,203] [INFO] Task started: fastANI
[2024-01-24 14:31:12,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0bbce6-6820-4797-a9a4-e7bc518bf99c/GCF_905410075.1_ASM90541007v1_genomic.fna.gz --refList GCF_905410075.1_ASM90541007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_905410075.1_ASM90541007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:15,934] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:15,943] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:15,944] [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_001457695.1	s__Campylobacter_D jejuni	99.9981	552	553	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.50	95.69	0.92	0.84	1918	conclusive
GCA_014305285.1	s__Campylobacter_D jejuni_D	94.0883	469	553	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000163995.1	s__Campylobacter_D jejuni_A	90.872	480	553	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_000254135.1	s__Campylobacter_D coli	85.7499	417	553	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.69	96.32	0.91	0.84	983	-
GCF_001687475.2	s__Campylobacter_D hepaticus	83.909	407	553	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_009362725.1	s__Campylobacter_D hepaticus_A	83.6448	400	553	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000470055.1	s__Campylobacter_D coli_A	83.0501	427	553	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	97.85	97.41	0.95	0.91	86	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	82.7427	422	553	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 14:31:15,946] [INFO] GTDB search result was written to GCF_905410075.1_ASM90541007v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:15,946] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:15,949] [INFO] DFAST_QC result json was written to GCF_905410075.1_ASM90541007v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:15,949] [INFO] DFAST_QC completed!
[2024-01-24 14:31:15,949] [INFO] Total running time: 0h0m29s