[2023-06-29 20:34:23,036] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:34:23,038] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:34:23,038] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference
[2023-06-29 20:34:24,292] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:34:24,296] [INFO] Task started: Prodigal
[2023-06-29 20:34:24,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg81041d11-b610-41b6-bd91-f9deebe3593e/GCA_011050175.1_ASM1105017v1_genomic.fna.gz | prodigal -d GCA_011050175.1_ASM1105017v1_genomic.fna/cds.fna -a GCA_011050175.1_ASM1105017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:34:26,611] [INFO] Task succeeded: Prodigal
[2023-06-29 20:34:26,611] [INFO] Task started: HMMsearch
[2023-06-29 20:34:26,611] [INFO] Running command: hmmsearch --tblout GCA_011050175.1_ASM1105017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/reference_markers.hmm GCA_011050175.1_ASM1105017v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:34:26,826] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:34:26,828] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg81041d11-b610-41b6-bd91-f9deebe3593e/GCA_011050175.1_ASM1105017v1_genomic.fna.gz]
[2023-06-29 20:34:26,847] [INFO] Query marker FASTA was written to GCA_011050175.1_ASM1105017v1_genomic.fna/markers.fasta
[2023-06-29 20:34:26,847] [INFO] Task started: Blastn
[2023-06-29 20:34:26,848] [INFO] Running command: blastn -query GCA_011050175.1_ASM1105017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/reference_markers.fasta -out GCA_011050175.1_ASM1105017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:27,339] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:27,343] [INFO] Selected 5 target genomes.
[2023-06-29 20:34:27,343] [INFO] Target genome list was writen to GCA_011050175.1_ASM1105017v1_genomic.fna/target_genomes.txt
[2023-06-29 20:34:27,345] [INFO] Task started: fastANI
[2023-06-29 20:34:27,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg81041d11-b610-41b6-bd91-f9deebe3593e/GCA_011050175.1_ASM1105017v1_genomic.fna.gz --refList GCA_011050175.1_ASM1105017v1_genomic.fna/target_genomes.txt --output GCA_011050175.1_ASM1105017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:34:29,398] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:29,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:34:29,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:34:29,406] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:34:29,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:34:29,406] [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
Thermococcus aciditolerans	strain=SY113	GCA_008152015.1	2598455	2598455	type	True	84.9011	242	280	95	below_threshold
Thermococcus celericrescens	strain=DSM 17994	GCA_001484195.1	227598	227598	type	True	84.8409	238	280	95	below_threshold
Thermococcus indicus	strain=IOH1	GCA_006274605.1	2586643	2586643	type	True	84.6416	239	280	95	below_threshold
Thermococcus camini	strain=IRI35c	GCA_904067545.1	2016373	2016373	type	True	84.3082	241	280	95	below_threshold
Thermococcus siculi	strain=RG-20	GCA_002214505.1	72803	72803	type	True	81.2623	215	280	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:34:29,408] [INFO] DFAST Taxonomy check result was written to GCA_011050175.1_ASM1105017v1_genomic.fna/tc_result.tsv
[2023-06-29 20:34:29,409] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:34:29,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:34:29,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/checkm_data
[2023-06-29 20:34:29,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:34:29,429] [INFO] Task started: CheckM
[2023-06-29 20:34:29,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011050175.1_ASM1105017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011050175.1_ASM1105017v1_genomic.fna/checkm_input GCA_011050175.1_ASM1105017v1_genomic.fna/checkm_result
[2023-06-29 20:34:44,776] [INFO] Task succeeded: CheckM
[2023-06-29 20:34:44,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:34:44,804] [INFO] ===== Completeness check finished =====
[2023-06-29 20:34:44,804] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:34:44,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011050175.1_ASM1105017v1_genomic.fna/markers.fasta)
[2023-06-29 20:34:44,805] [INFO] Task started: Blastn
[2023-06-29 20:34:44,805] [INFO] Running command: blastn -query GCA_011050175.1_ASM1105017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa71e32b-d936-49a9-a823-9056d51da4ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_011050175.1_ASM1105017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:45,276] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:45,281] [INFO] Selected 5 target genomes.
[2023-06-29 20:34:45,281] [INFO] Target genome list was writen to GCA_011050175.1_ASM1105017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:34:45,311] [INFO] Task started: fastANI
[2023-06-29 20:34:45,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg81041d11-b610-41b6-bd91-f9deebe3593e/GCA_011050175.1_ASM1105017v1_genomic.fna.gz --refList GCA_011050175.1_ASM1105017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011050175.1_ASM1105017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:34:47,333] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:47,345] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:34:47,345] [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_011050175.1	s__Thermococcus sp011050175	100.0	275	280	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012027645.1	s__Thermococcus sp012027645	85.52	245	280	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484195.1	s__Thermococcus celericrescens	84.8409	238	280	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_006274605.1	s__Thermococcus indicus	84.6416	239	280	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904067545.1	s__Thermococcus camini	84.3391	240	280	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:34:47,347] [INFO] GTDB search result was written to GCA_011050175.1_ASM1105017v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:34:47,348] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:34:47,352] [INFO] DFAST_QC result json was written to GCA_011050175.1_ASM1105017v1_genomic.fna/dqc_result.json
[2023-06-29 20:34:47,352] [INFO] DFAST_QC completed!
[2023-06-29 20:34:47,353] [INFO] Total running time: 0h0m24s