[2024-01-24 13:25:29,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference
[2024-01-24 13:25:31,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,220] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,220] [INFO] Running command: gunzip -c /var/lib/cwl/stge4286771-e0c3-41d9-a0ff-f6f348e565e6/GCF_008152015.1_ASM815201v1_genomic.fna.gz | prodigal -d GCF_008152015.1_ASM815201v1_genomic.fna/cds.fna -a GCF_008152015.1_ASM815201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:36,636] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:36,637] [INFO] Task started: HMMsearch
[2024-01-24 13:25:36,637] [INFO] Running command: hmmsearch --tblout GCF_008152015.1_ASM815201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/reference_markers.hmm GCF_008152015.1_ASM815201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:36,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:36,885] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge4286771-e0c3-41d9-a0ff-f6f348e565e6/GCF_008152015.1_ASM815201v1_genomic.fna.gz]
[2024-01-24 13:25:36,912] [INFO] Query marker FASTA was written to GCF_008152015.1_ASM815201v1_genomic.fna/markers.fasta
[2024-01-24 13:25:36,912] [INFO] Task started: Blastn
[2024-01-24 13:25:36,913] [INFO] Running command: blastn -query GCF_008152015.1_ASM815201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/reference_markers.fasta -out GCF_008152015.1_ASM815201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:37,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:37,444] [INFO] Selected 5 target genomes.
[2024-01-24 13:25:37,445] [INFO] Target genome list was writen to GCF_008152015.1_ASM815201v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:37,450] [INFO] Task started: fastANI
[2024-01-24 13:25:37,450] [INFO] Running command: fastANI --query /var/lib/cwl/stge4286771-e0c3-41d9-a0ff-f6f348e565e6/GCF_008152015.1_ASM815201v1_genomic.fna.gz --refList GCF_008152015.1_ASM815201v1_genomic.fna/target_genomes.txt --output GCF_008152015.1_ASM815201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:40,516] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:40,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:40,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:40,526] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:40,526] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:25:40,526] [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	100.0	720	721	95	inconclusive
Thermococcus celericrescens	strain=DSM 17994	GCA_001484195.1	227598	227598	type	True	95.6779	600	721	95	inconclusive
Thermococcus indicus	strain=IOH1	GCA_006274605.1	2586643	2586643	type	True	91.9343	593	721	95	below_threshold
Thermococcus camini	strain=IRI35c	GCA_904067545.1	2016373	2016373	type	True	89.7844	540	721	95	below_threshold
Thermococcus radiotolerans	strain=EJ2	GCA_002214565.1	187880	187880	type	True	86.4441	474	721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:40,527] [INFO] DFAST Taxonomy check result was written to GCF_008152015.1_ASM815201v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:40,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:40,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:40,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/checkm_data
[2024-01-24 13:25:40,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:40,551] [INFO] Task started: CheckM
[2024-01-24 13:25:40,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008152015.1_ASM815201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008152015.1_ASM815201v1_genomic.fna/checkm_input GCF_008152015.1_ASM815201v1_genomic.fna/checkm_result
[2024-01-24 13:26:03,828] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:03,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:03,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:03,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:03,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008152015.1_ASM815201v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:03,852] [INFO] Task started: Blastn
[2024-01-24 13:26:03,852] [INFO] Running command: blastn -query GCF_008152015.1_ASM815201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc295ca6-32cf-41e8-b58a-aaec1f534449/dqc_reference/reference_markers_gtdb.fasta -out GCF_008152015.1_ASM815201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:04,396] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:04,399] [INFO] Selected 6 target genomes.
[2024-01-24 13:26:04,400] [INFO] Target genome list was writen to GCF_008152015.1_ASM815201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:04,405] [INFO] Task started: fastANI
[2024-01-24 13:26:04,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge4286771-e0c3-41d9-a0ff-f6f348e565e6/GCF_008152015.1_ASM815201v1_genomic.fna.gz --refList GCF_008152015.1_ASM815201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008152015.1_ASM815201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:07,825] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,836] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:07,836] [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_001484195.1	s__Thermococcus celericrescens	95.6536	601	721	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	95.67	95.67	0.83	0.83	2	conclusive
GCF_012027495.1	s__Thermococcus sp012027495	93.343	604	721	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_006274605.1	s__Thermococcus indicus	91.9308	593	721	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_000221185.1	s__Thermococcus sp000221185	91.2197	547	721	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_012027645.1	s__Thermococcus sp012027645	90.9547	535	721	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	89.7844	540	721	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,838] [INFO] GTDB search result was written to GCF_008152015.1_ASM815201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:07,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:07,841] [INFO] DFAST_QC result json was written to GCF_008152015.1_ASM815201v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:07,841] [INFO] DFAST_QC completed!
[2024-01-24 13:26:07,842] [INFO] Total running time: 0h0m38s