[2023-06-30 01:23:19,036] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:23:19,043] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:23:19,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference
[2023-06-30 01:23:20,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:23:20,444] [INFO] Task started: Prodigal
[2023-06-30 01:23:20,444] [INFO] Running command: gunzip -c /var/lib/cwl/stgaec143a3-2939-47fb-b4dd-9251486b51aa/GCA_024281175.1_ASM2428117v1_genomic.fna.gz | prodigal -d GCA_024281175.1_ASM2428117v1_genomic.fna/cds.fna -a GCA_024281175.1_ASM2428117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:23:24,428] [INFO] Task succeeded: Prodigal
[2023-06-30 01:23:24,428] [INFO] Task started: HMMsearch
[2023-06-30 01:23:24,428] [INFO] Running command: hmmsearch --tblout GCA_024281175.1_ASM2428117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/reference_markers.hmm GCA_024281175.1_ASM2428117v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:23:24,755] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:23:24,757] [INFO] Found 6/6 markers.
[2023-06-30 01:23:24,791] [INFO] Query marker FASTA was written to GCA_024281175.1_ASM2428117v1_genomic.fna/markers.fasta
[2023-06-30 01:23:24,792] [INFO] Task started: Blastn
[2023-06-30 01:23:24,792] [INFO] Running command: blastn -query GCA_024281175.1_ASM2428117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/reference_markers.fasta -out GCA_024281175.1_ASM2428117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:23:25,482] [INFO] Task succeeded: Blastn
[2023-06-30 01:23:25,487] [INFO] Selected 12 target genomes.
[2023-06-30 01:23:25,487] [INFO] Target genome list was writen to GCA_024281175.1_ASM2428117v1_genomic.fna/target_genomes.txt
[2023-06-30 01:23:25,493] [INFO] Task started: fastANI
[2023-06-30 01:23:25,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgaec143a3-2939-47fb-b4dd-9251486b51aa/GCA_024281175.1_ASM2428117v1_genomic.fna.gz --refList GCA_024281175.1_ASM2428117v1_genomic.fna/target_genomes.txt --output GCA_024281175.1_ASM2428117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:23:28,626] [INFO] Task succeeded: fastANI
[2023-06-30 01:23:28,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:23:28,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:23:28,637] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:23:28,637] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 01:23:28,637] [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	75.8608	60	717	95	below_threshold
Aliarcobacter butzleri	strain=LMG 10828	GCA_024584145.1	28197	28197	type	True	75.8062	56	717	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	75.7987	60	717	95	below_threshold
Aliarcobacter skirrowii	strain=NCTC12713	GCA_900445295.1	28200	28200	type	True	75.7233	57	717	95	below_threshold
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_003544835.1	28200	28200	type	True	75.6788	59	717	95	below_threshold
Aliarcobacter skirrowii	strain=CCUG 10374	GCA_008802155.1	28200	28200	type	True	75.6473	54	717	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	75.6239	55	717	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	75.6239	55	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 01:23:28,643] [INFO] DFAST Taxonomy check result was written to GCA_024281175.1_ASM2428117v1_genomic.fna/tc_result.tsv
[2023-06-30 01:23:28,643] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:23:28,643] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:23:28,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/checkm_data
[2023-06-30 01:23:28,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:23:28,677] [INFO] Task started: CheckM
[2023-06-30 01:23:28,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024281175.1_ASM2428117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024281175.1_ASM2428117v1_genomic.fna/checkm_input GCA_024281175.1_ASM2428117v1_genomic.fna/checkm_result
[2023-06-30 01:23:49,562] [INFO] Task succeeded: CheckM
[2023-06-30 01:23:49,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:23:49,590] [INFO] ===== Completeness check finished =====
[2023-06-30 01:23:49,591] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:23:49,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024281175.1_ASM2428117v1_genomic.fna/markers.fasta)
[2023-06-30 01:23:49,593] [INFO] Task started: Blastn
[2023-06-30 01:23:49,593] [INFO] Running command: blastn -query GCA_024281175.1_ASM2428117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e706f39-2db4-476e-bf91-8410fb21234e/dqc_reference/reference_markers_gtdb.fasta -out GCA_024281175.1_ASM2428117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:23:50,431] [INFO] Task succeeded: Blastn
[2023-06-30 01:23:50,435] [INFO] Selected 15 target genomes.
[2023-06-30 01:23:50,435] [INFO] Target genome list was writen to GCA_024281175.1_ASM2428117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:23:50,452] [INFO] Task started: fastANI
[2023-06-30 01:23:50,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgaec143a3-2939-47fb-b4dd-9251486b51aa/GCA_024281175.1_ASM2428117v1_genomic.fna.gz --refList GCA_024281175.1_ASM2428117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024281175.1_ASM2428117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:23:57,249] [INFO] Task succeeded: fastANI
[2023-06-30 01:23:57,253] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 01:23:57,253] [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
GCA_000276965.1	s__Thiovulum sp000276965	77.8378	175	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Thiovulaceae;g__Thiovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187115.1	s__Aliarcobacter butzleri	75.8387	61	717	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
--------------------------------------------------------------------------------
[2023-06-30 01:23:57,255] [INFO] GTDB search result was written to GCA_024281175.1_ASM2428117v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:23:57,256] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:23:57,259] [INFO] DFAST_QC result json was written to GCA_024281175.1_ASM2428117v1_genomic.fna/dqc_result.json
[2023-06-30 01:23:57,259] [INFO] DFAST_QC completed!
[2023-06-30 01:23:57,259] [INFO] Total running time: 0h0m38s