[2024-01-24 15:18:27,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference
[2024-01-24 15:18:28,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,814] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg71497ce6-3ab9-45cf-b789-958ecb3402f9/GCF_018228765.1_ASM1822876v1_genomic.fna.gz | prodigal -d GCF_018228765.1_ASM1822876v1_genomic.fna/cds.fna -a GCF_018228765.1_ASM1822876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:42,754] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:42,754] [INFO] Task started: HMMsearch
[2024-01-24 15:18:42,754] [INFO] Running command: hmmsearch --tblout GCF_018228765.1_ASM1822876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/reference_markers.hmm GCF_018228765.1_ASM1822876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:43,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:43,038] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg71497ce6-3ab9-45cf-b789-958ecb3402f9/GCF_018228765.1_ASM1822876v1_genomic.fna.gz]
[2024-01-24 15:18:43,065] [INFO] Query marker FASTA was written to GCF_018228765.1_ASM1822876v1_genomic.fna/markers.fasta
[2024-01-24 15:18:43,066] [INFO] Task started: Blastn
[2024-01-24 15:18:43,066] [INFO] Running command: blastn -query GCF_018228765.1_ASM1822876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/reference_markers.fasta -out GCF_018228765.1_ASM1822876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:43,652] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:43,655] [INFO] Selected 6 target genomes.
[2024-01-24 15:18:43,656] [INFO] Target genome list was writen to GCF_018228765.1_ASM1822876v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:43,659] [INFO] Task started: fastANI
[2024-01-24 15:18:43,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg71497ce6-3ab9-45cf-b789-958ecb3402f9/GCF_018228765.1_ASM1822876v1_genomic.fna.gz --refList GCF_018228765.1_ASM1822876v1_genomic.fna/target_genomes.txt --output GCF_018228765.1_ASM1822876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:52,268] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:52,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:52,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:52,281] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:52,282] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:52,282] [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
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	93.3604	845	1007	95	below_threshold
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	93.3439	845	1007	95	below_threshold
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	93.2657	829	1007	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	89.6351	801	1007	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	89.6075	773	1007	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	89.3193	798	1007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:52,289] [INFO] DFAST Taxonomy check result was written to GCF_018228765.1_ASM1822876v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:52,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:52,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:52,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/checkm_data
[2024-01-24 15:18:52,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:52,332] [INFO] Task started: CheckM
[2024-01-24 15:18:52,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018228765.1_ASM1822876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018228765.1_ASM1822876v1_genomic.fna/checkm_input GCF_018228765.1_ASM1822876v1_genomic.fna/checkm_result
[2024-01-24 15:19:32,120] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:32,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,141] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:32,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:32,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018228765.1_ASM1822876v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:32,143] [INFO] Task started: Blastn
[2024-01-24 15:19:32,143] [INFO] Running command: blastn -query GCF_018228765.1_ASM1822876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c7a4bc-f796-45d6-b679-1fcab78f122b/dqc_reference/reference_markers_gtdb.fasta -out GCF_018228765.1_ASM1822876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:32,641] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:32,644] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:32,644] [INFO] Target genome list was writen to GCF_018228765.1_ASM1822876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:32,651] [INFO] Task started: fastANI
[2024-01-24 15:19:32,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg71497ce6-3ab9-45cf-b789-958ecb3402f9/GCF_018228765.1_ASM1822876v1_genomic.fna.gz --refList GCF_018228765.1_ASM1822876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018228765.1_ASM1822876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:44,966] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:44,981] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:44,982] [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_018228765.1	s__Halorubrum sp000296615	100.0	1007	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.09	99.09	0.95	0.95	2	conclusive
GCF_003666015.1	s__Halorubrum sp003666015	94.4317	855	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337335.1	s__Halorubrum distributum	93.3555	846	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.52	97.80	0.88	0.83	7	-
GCF_002355655.1	s__Halorubrum trapanicum_A	93.0503	857	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336875.1	s__Halorubrum californiense	91.0939	786	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_001280455.1	s__Halorubrum tropicale	90.6165	814	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	97.18	95.21	0.82	0.77	8	-
GCF_017873555.1	s__Halorubrum trapanicum	90.5177	778	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337075.1	s__Halorubrum hochstenium	89.1696	784	1007	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.2282	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:44,983] [INFO] GTDB search result was written to GCF_018228765.1_ASM1822876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:44,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:44,988] [INFO] DFAST_QC result json was written to GCF_018228765.1_ASM1822876v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:44,988] [INFO] DFAST_QC completed!
[2024-01-24 15:19:44,988] [INFO] Total running time: 0h1m18s