[2024-01-24 10:47:40,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,786] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg88efd154-81e4-4473-afd4-317a5bba6e95/GCF_003063295.1_ASM306329v1_genomic.fna.gz | prodigal -d GCF_003063295.1_ASM306329v1_genomic.fna/cds.fna -a GCF_003063295.1_ASM306329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:48,231] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:48,232] [INFO] Task started: HMMsearch
[2024-01-24 10:47:48,232] [INFO] Running command: hmmsearch --tblout GCF_003063295.1_ASM306329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/reference_markers.hmm GCF_003063295.1_ASM306329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:48,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:48,565] [INFO] Found 6/6 markers.
[2024-01-24 10:47:48,591] [INFO] Query marker FASTA was written to GCF_003063295.1_ASM306329v1_genomic.fna/markers.fasta
[2024-01-24 10:47:48,593] [INFO] Task started: Blastn
[2024-01-24 10:47:48,593] [INFO] Running command: blastn -query GCF_003063295.1_ASM306329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/reference_markers.fasta -out GCF_003063295.1_ASM306329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,832] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,837] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:50,837] [INFO] Target genome list was writen to GCF_003063295.1_ASM306329v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:51,106] [INFO] Task started: fastANI
[2024-01-24 10:47:51,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg88efd154-81e4-4473-afd4-317a5bba6e95/GCF_003063295.1_ASM306329v1_genomic.fna.gz --refList GCF_003063295.1_ASM306329v1_genomic.fna/target_genomes.txt --output GCF_003063295.1_ASM306329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,177] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,194] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:58,194] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:58,195] [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
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	94.5405	609	728	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	94.5261	609	728	95	below_threshold
Aliarcobacter butzleri	strain=LMG 10828	GCA_024584145.1	28197	28197	type	True	94.4009	611	728	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	84.6496	519	728	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	84.6333	530	728	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	84.4231	524	728	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	84.3514	527	728	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	83.5391	492	728	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	83.5157	495	728	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	82.3553	435	728	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	82.2051	453	728	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	81.1284	397	728	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	81.1193	396	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,196] [INFO] DFAST Taxonomy check result was written to GCF_003063295.1_ASM306329v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/checkm_data
[2024-01-24 10:47:58,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,222] [INFO] Task started: CheckM
[2024-01-24 10:47:58,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003063295.1_ASM306329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003063295.1_ASM306329v1_genomic.fna/checkm_input GCF_003063295.1_ASM306329v1_genomic.fna/checkm_result
[2024-01-24 10:48:17,231] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:17,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:17,251] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:17,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:17,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003063295.1_ASM306329v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:17,252] [INFO] Task started: Blastn
[2024-01-24 10:48:17,252] [INFO] Running command: blastn -query GCF_003063295.1_ASM306329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab6d09f3-9572-4727-839b-8342aba2bda1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003063295.1_ASM306329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:18,481] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:18,486] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:18,487] [INFO] Target genome list was writen to GCF_003063295.1_ASM306329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:18,497] [INFO] Task started: fastANI
[2024-01-24 10:48:18,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg88efd154-81e4-4473-afd4-317a5bba6e95/GCF_003063295.1_ASM306329v1_genomic.fna.gz --refList GCF_003063295.1_ASM306329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003063295.1_ASM306329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:24,598] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:24,614] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:24,614] [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_003063295.1	s__Aliarcobacter lacus	100.0	727	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900187115.1	s__Aliarcobacter butzleri	94.5261	609	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_013201725.1	s__Aliarcobacter defluvii	84.6718	528	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_003544915.1	s__Aliarcobacter ellisii	84.4131	524	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	83.5519	493	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201935.1	s__Aliarcobacter cloacae	83.1965	496	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_003316695.1	s__Aliarcobacter sp003316695	82.9204	482	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013201705.1	s__Aliarcobacter faecis	82.1866	453	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	81.7233	424	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_003544835.1	s__Aliarcobacter skirrowii	81.2004	403	728	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:24,616] [INFO] GTDB search result was written to GCF_003063295.1_ASM306329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:24,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:24,621] [INFO] DFAST_QC result json was written to GCF_003063295.1_ASM306329v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:24,621] [INFO] DFAST_QC completed!
[2024-01-24 10:48:24,621] [INFO] Total running time: 0h0m44s