[2024-01-24 14:42:02,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,712] [INFO] DQC Reference Directory: /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference
[2024-01-24 14:42:04,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:04,007] [INFO] Task started: Prodigal
[2024-01-24 14:42:04,007] [INFO] Running command: gunzip -c /var/lib/cwl/stg54bb5445-5a7a-4bf4-89cc-2797fd976e99/GCF_002080395.1_ASM208039v1_genomic.fna.gz | prodigal -d GCF_002080395.1_ASM208039v1_genomic.fna/cds.fna -a GCF_002080395.1_ASM208039v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:08,031] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:08,031] [INFO] Task started: HMMsearch
[2024-01-24 14:42:08,032] [INFO] Running command: hmmsearch --tblout GCF_002080395.1_ASM208039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/reference_markers.hmm GCF_002080395.1_ASM208039v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:08,269] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:08,272] [INFO] Found 6/6 markers.
[2024-01-24 14:42:08,296] [INFO] Query marker FASTA was written to GCF_002080395.1_ASM208039v1_genomic.fna/markers.fasta
[2024-01-24 14:42:08,297] [INFO] Task started: Blastn
[2024-01-24 14:42:08,297] [INFO] Running command: blastn -query GCF_002080395.1_ASM208039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/reference_markers.fasta -out GCF_002080395.1_ASM208039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:08,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:08,926] [INFO] Selected 6 target genomes.
[2024-01-24 14:42:08,926] [INFO] Target genome list was writen to GCF_002080395.1_ASM208039v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:08,935] [INFO] Task started: fastANI
[2024-01-24 14:42:08,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bb5445-5a7a-4bf4-89cc-2797fd976e99/GCF_002080395.1_ASM208039v1_genomic.fna.gz --refList GCF_002080395.1_ASM208039v1_genomic.fna/target_genomes.txt --output GCF_002080395.1_ASM208039v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:11,889] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:11,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:11,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:11,897] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:42:11,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:11,897] [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 helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	100.0	622	622	95	conclusive
Campylobacter helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	99.9976	621	622	95	conclusive
Campylobacter helveticus	strain=ATCC 51209	GCA_900176295.1	28898	28898	type	True	99.9345	571	622	95	conclusive
Campylobacter upsaliensis	strain=FDAARGOS_1518	GCA_020297605.1	28080	28080	type	True	86.3703	452	622	95	below_threshold
Campylobacter upsaliensis	strain=DSM 5365	GCA_000620965.1	28080	28080	type	True	86.2496	433	622	95	below_threshold
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	84.9761	420	622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:11,899] [INFO] DFAST Taxonomy check result was written to GCF_002080395.1_ASM208039v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:11,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:11,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:11,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/checkm_data
[2024-01-24 14:42:11,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:11,928] [INFO] Task started: CheckM
[2024-01-24 14:42:11,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002080395.1_ASM208039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002080395.1_ASM208039v1_genomic.fna/checkm_input GCF_002080395.1_ASM208039v1_genomic.fna/checkm_result
[2024-01-24 14:42:31,599] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:31,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:31,631] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:31,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:31,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002080395.1_ASM208039v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:31,633] [INFO] Task started: Blastn
[2024-01-24 14:42:31,633] [INFO] Running command: blastn -query GCF_002080395.1_ASM208039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd024408b-3d20-4fe7-8b60-cb93a0116937/dqc_reference/reference_markers_gtdb.fasta -out GCF_002080395.1_ASM208039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:32,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:32,548] [INFO] Selected 11 target genomes.
[2024-01-24 14:42:32,549] [INFO] Target genome list was writen to GCF_002080395.1_ASM208039v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:32,559] [INFO] Task started: fastANI
[2024-01-24 14:42:32,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bb5445-5a7a-4bf4-89cc-2797fd976e99/GCF_002080395.1_ASM208039v1_genomic.fna.gz --refList GCF_002080395.1_ASM208039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002080395.1_ASM208039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:37,041] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:37,052] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:37,052] [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_002080395.1	s__Campylobacter_D helveticus	100.0	622	622	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.44	98.95	0.97	0.95	14	conclusive
GCF_900637395.1	s__Campylobacter_D upsaliensis	86.2537	455	622	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_002738305.1	s__Campylobacter_D vulpis	84.9761	420	622	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.20	98.60	0.92	0.87	15	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	78.7999	237	622	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_001492295.1	s__Campylobacter_D coli_B	78.3963	251	622	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	98.33	0.93	0.85	59	-
GCA_014305285.1	s__Campylobacter_D jejuni_D	78.3327	221	622	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_000254135.1	s__Campylobacter_D coli	78.0738	231	622	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_004378855.1	s__Campylobacter_D sp004378855	78.0415	210	622	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_005406215.1	s__Campylobacter_D aviculae	77.8697	190	622	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_005406225.1	s__Campylobacter_D taeniopygiae	77.7311	207	622	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_005406205.1	s__Campylobacter_D estrildidarum	77.6969	192	622	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 14:42:37,054] [INFO] GTDB search result was written to GCF_002080395.1_ASM208039v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:37,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:37,057] [INFO] DFAST_QC result json was written to GCF_002080395.1_ASM208039v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:37,058] [INFO] DFAST_QC completed!
[2024-01-24 14:42:37,058] [INFO] Total running time: 0h0m34s