[2024-01-24 13:37:27,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference
[2024-01-24 13:37:29,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,122] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a13d735-1fcf-46e7-b3f1-5bd5fa4df847/GCF_000022545.1_ASM2254v1_genomic.fna.gz | prodigal -d GCF_000022545.1_ASM2254v1_genomic.fna/cds.fna -a GCF_000022545.1_ASM2254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:33,183] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:33,184] [INFO] Task started: HMMsearch
[2024-01-24 13:37:33,184] [INFO] Running command: hmmsearch --tblout GCF_000022545.1_ASM2254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/reference_markers.hmm GCF_000022545.1_ASM2254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:33,391] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:33,393] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8a13d735-1fcf-46e7-b3f1-5bd5fa4df847/GCF_000022545.1_ASM2254v1_genomic.fna.gz]
[2024-01-24 13:37:33,415] [INFO] Query marker FASTA was written to GCF_000022545.1_ASM2254v1_genomic.fna/markers.fasta
[2024-01-24 13:37:33,416] [INFO] Task started: Blastn
[2024-01-24 13:37:33,416] [INFO] Running command: blastn -query GCF_000022545.1_ASM2254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/reference_markers.fasta -out GCF_000022545.1_ASM2254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:33,910] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:33,914] [INFO] Selected 5 target genomes.
[2024-01-24 13:37:33,914] [INFO] Target genome list was writen to GCF_000022545.1_ASM2254v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:33,939] [INFO] Task started: fastANI
[2024-01-24 13:37:33,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a13d735-1fcf-46e7-b3f1-5bd5fa4df847/GCF_000022545.1_ASM2254v1_genomic.fna.gz --refList GCF_000022545.1_ASM2254v1_genomic.fna/target_genomes.txt --output GCF_000022545.1_ASM2254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,885] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:35,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:35,885] [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 sibiricus	strain=MM 739	GCA_000022545.1	172049	172049	type	True	100.0	615	615	95	conclusive
Thermococcus aggregans	strain=TY	GCA_024022995.1	110163	110163	type	True	81.2149	290	615	95	below_threshold
Thermococcus alcaliphilus	strain=AEDII12	GCA_024054535.1	139207	139207	type	True	78.7608	247	615	95	below_threshold
Thermococcus litoralis	strain=DSM 5473	GCA_000246985.3	2265	2265	type	True	78.5322	260	615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,887] [INFO] DFAST Taxonomy check result was written to GCF_000022545.1_ASM2254v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/checkm_data
[2024-01-24 13:37:35,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:35,910] [INFO] Task started: CheckM
[2024-01-24 13:37:35,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000022545.1_ASM2254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000022545.1_ASM2254v1_genomic.fna/checkm_input GCF_000022545.1_ASM2254v1_genomic.fna/checkm_result
[2024-01-24 13:37:55,332] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:55,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:55,351] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:55,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:55,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000022545.1_ASM2254v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:55,352] [INFO] Task started: Blastn
[2024-01-24 13:37:55,353] [INFO] Running command: blastn -query GCF_000022545.1_ASM2254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9d0efe-d4f3-44ea-b8b0-e568ea86248e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000022545.1_ASM2254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:55,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:55,860] [INFO] Selected 6 target genomes.
[2024-01-24 13:37:55,860] [INFO] Target genome list was writen to GCF_000022545.1_ASM2254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:55,989] [INFO] Task started: fastANI
[2024-01-24 13:37:55,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a13d735-1fcf-46e7-b3f1-5bd5fa4df847/GCF_000022545.1_ASM2254v1_genomic.fna.gz --refList GCF_000022545.1_ASM2254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000022545.1_ASM2254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:58,451] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:58,462] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:58,462] [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_000022545.1	s__Thermococcus_A sibiricus	100.0	615	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.36	98.17	0.89	0.84	5	conclusive
GCA_003663535.1	s__Thermococcus_A sp003663535	91.5094	304	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003663525.1	s__Thermococcus_A sp003663525	91.0966	338	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.62	98.62	0.75	0.75	2	-
GCF_001484685.1	s__Thermococcus_A sp001484685	78.6464	200	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.39	98.39	0.89	0.89	2	-
GCF_000246985.2	s__Thermococcus_A litoralis	78.5162	261	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.93	96.93	0.89	0.89	2	-
GCA_017656495.1	s__Thermococcus_B sp017656495	76.8321	91	615	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,464] [INFO] GTDB search result was written to GCF_000022545.1_ASM2254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:58,464] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:58,467] [INFO] DFAST_QC result json was written to GCF_000022545.1_ASM2254v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:58,468] [INFO] DFAST_QC completed!
[2024-01-24 13:37:58,468] [INFO] Total running time: 0h0m31s