[2024-01-25 19:42:50,812] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:50,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:50,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference
[2024-01-25 19:42:52,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:52,015] [INFO] Task started: Prodigal
[2024-01-25 19:42:52,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cd7893a-cfe8-4063-bc85-74b835415d39/GCF_017873335.1_ASM1787333v1_genomic.fna.gz | prodigal -d GCF_017873335.1_ASM1787333v1_genomic.fna/cds.fna -a GCF_017873335.1_ASM1787333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:56,248] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:56,248] [INFO] Task started: HMMsearch
[2024-01-25 19:42:56,249] [INFO] Running command: hmmsearch --tblout GCF_017873335.1_ASM1787333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/reference_markers.hmm GCF_017873335.1_ASM1787333v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:56,426] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:56,427] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9cd7893a-cfe8-4063-bc85-74b835415d39/GCF_017873335.1_ASM1787333v1_genomic.fna.gz]
[2024-01-25 19:42:56,446] [INFO] Query marker FASTA was written to GCF_017873335.1_ASM1787333v1_genomic.fna/markers.fasta
[2024-01-25 19:42:56,447] [INFO] Task started: Blastn
[2024-01-25 19:42:56,447] [INFO] Running command: blastn -query GCF_017873335.1_ASM1787333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/reference_markers.fasta -out GCF_017873335.1_ASM1787333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:56,915] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:56,918] [INFO] Selected 7 target genomes.
[2024-01-25 19:42:56,918] [INFO] Target genome list was writen to GCF_017873335.1_ASM1787333v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:56,922] [INFO] Task started: fastANI
[2024-01-25 19:42:56,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd7893a-cfe8-4063-bc85-74b835415d39/GCF_017873335.1_ASM1787333v1_genomic.fna.gz --refList GCF_017873335.1_ASM1787333v1_genomic.fna/target_genomes.txt --output GCF_017873335.1_ASM1787333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:00,387] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:00,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:00,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:00,393] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:00,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:00,394] [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 stetteri	strain=DSM 5262	GCA_017873335.1	49900	49900	type	True	100.0	673	674	95	conclusive
Thermococcus kodakarensis	strain=KOD1	GCA_000009965.1	311400	311400	type	True	85.6511	506	674	95	below_threshold
Thermococcus peptonophilus	strain=OG-1	GCA_001592435.1	53952	53952	type	True	85.358	485	674	95	below_threshold
Thermococcus siculi	strain=RG-20	GCA_002214505.1	72803	72803	type	True	80.7627	345	674	95	below_threshold
Thermococcus nautili	strain=30-1	GCA_000585495.1	195522	195522	type	True	80.2523	340	674	95	below_threshold
Thermococcus henrietii	strain=EXT12c	GCA_900198835.1	2016361	2016361	type	True	80.0104	330	674	95	below_threshold
Thermococcus zilligii	strain=AN1	GCA_000258515.1	54076	54076	type	True	79.1264	300	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:00,395] [INFO] DFAST Taxonomy check result was written to GCF_017873335.1_ASM1787333v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:00,396] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:00,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:00,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/checkm_data
[2024-01-25 19:43:00,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:00,421] [INFO] Task started: CheckM
[2024-01-25 19:43:00,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873335.1_ASM1787333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873335.1_ASM1787333v1_genomic.fna/checkm_input GCF_017873335.1_ASM1787333v1_genomic.fna/checkm_result
[2024-01-25 19:43:18,456] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:18,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:18,481] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:18,482] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:18,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873335.1_ASM1787333v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:18,482] [INFO] Task started: Blastn
[2024-01-25 19:43:18,482] [INFO] Running command: blastn -query GCF_017873335.1_ASM1787333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4bdb590-1c29-4f96-b796-6de0087343a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873335.1_ASM1787333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:18,985] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:18,988] [INFO] Selected 7 target genomes.
[2024-01-25 19:43:18,988] [INFO] Target genome list was writen to GCF_017873335.1_ASM1787333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:18,994] [INFO] Task started: fastANI
[2024-01-25 19:43:18,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd7893a-cfe8-4063-bc85-74b835415d39/GCF_017873335.1_ASM1787333v1_genomic.fna.gz --refList GCF_017873335.1_ASM1787333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873335.1_ASM1787333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:22,452] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:22,458] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:22,458] [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_017873335.1	s__Thermococcus stetteri	100.0	673	674	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_000009965.1	s__Thermococcus kodakarensis	85.6511	506	674	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.75	97.75	0.93	0.93	2	-
GCF_001592435.1	s__Thermococcus peptonophilus	85.3313	487	674	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.53	99.53	0.99	0.99	2	-
GCF_002214505.1	s__Thermococcus siculi	80.7559	345	674	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_012027595.1	s__Thermococcus sp012027595	80.7428	354	674	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_000585495.1	s__Thermococcus nautili	80.253	340	674	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000151205.2	s__Thermococcus sp000151205	79.7465	340	674	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:22,460] [INFO] GTDB search result was written to GCF_017873335.1_ASM1787333v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:22,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:22,462] [INFO] DFAST_QC result json was written to GCF_017873335.1_ASM1787333v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:22,463] [INFO] DFAST_QC completed!
[2024-01-25 19:43:22,463] [INFO] Total running time: 0h0m32s