[2024-01-24 12:31:33,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference
[2024-01-24 12:31:34,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,500] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg20693c8e-5548-4524-9d58-8197c33cc43c/GCF_001562425.1_ASM156242v1_genomic.fna.gz | prodigal -d GCF_001562425.1_ASM156242v1_genomic.fna/cds.fna -a GCF_001562425.1_ASM156242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:39,451] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:39,452] [INFO] Task started: HMMsearch
[2024-01-24 12:31:39,452] [INFO] Running command: hmmsearch --tblout GCF_001562425.1_ASM156242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/reference_markers.hmm GCF_001562425.1_ASM156242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:39,700] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:39,700] [INFO] Found 6/6 markers.
[2024-01-24 12:31:39,721] [INFO] Query marker FASTA was written to GCF_001562425.1_ASM156242v1_genomic.fna/markers.fasta
[2024-01-24 12:31:39,722] [INFO] Task started: Blastn
[2024-01-24 12:31:39,722] [INFO] Running command: blastn -query GCF_001562425.1_ASM156242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/reference_markers.fasta -out GCF_001562425.1_ASM156242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:40,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:40,251] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:40,251] [INFO] Target genome list was writen to GCF_001562425.1_ASM156242v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:40,298] [INFO] Task started: fastANI
[2024-01-24 12:31:40,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg20693c8e-5548-4524-9d58-8197c33cc43c/GCF_001562425.1_ASM156242v1_genomic.fna.gz --refList GCF_001562425.1_ASM156242v1_genomic.fna/target_genomes.txt --output GCF_001562425.1_ASM156242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:51,642] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:51,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:51,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:51,649] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:51,649] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:51,649] [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
Thermovenabulum gondwanense	strain=R270	GCA_001601575.1	520767	520767	type	True	78.9602	54	768	95	below_threshold
Thermosediminibacter litoriperuensis	strain=DSM 16647	GCA_008124715.1	291989	291989	type	True	78.6722	235	768	95	below_threshold
Thermosediminibacter oceani	strain=DSM 16646	GCA_000144645.1	291990	291990	type	True	78.5992	229	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,652] [INFO] DFAST Taxonomy check result was written to GCF_001562425.1_ASM156242v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:51,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:51,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:51,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/checkm_data
[2024-01-24 12:31:51,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:51,684] [INFO] Task started: CheckM
[2024-01-24 12:31:51,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001562425.1_ASM156242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001562425.1_ASM156242v1_genomic.fna/checkm_input GCF_001562425.1_ASM156242v1_genomic.fna/checkm_result
[2024-01-24 12:32:11,111] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:11,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,132] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:11,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:11,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001562425.1_ASM156242v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:11,132] [INFO] Task started: Blastn
[2024-01-24 12:32:11,132] [INFO] Running command: blastn -query GCF_001562425.1_ASM156242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb494f067-31cd-444a-ad89-021d6ac92e1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001562425.1_ASM156242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,852] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,855] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:11,855] [INFO] Target genome list was writen to GCF_001562425.1_ASM156242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:11,866] [INFO] Task started: fastANI
[2024-01-24 12:32:11,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg20693c8e-5548-4524-9d58-8197c33cc43c/GCF_001562425.1_ASM156242v1_genomic.fna.gz --refList GCF_001562425.1_ASM156242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001562425.1_ASM156242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:18,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:18,601] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:18,601] [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_001562425.1	s__Fervidicola ferrireducens	100.0	761	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__Fervidicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142995.1	s__Caldanaerovirga acetigignens	89.3141	560	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__Caldanaerovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242255.1	s__ZC4RG34 sp003242255	81.2437	324	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__ZC4RG34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001601575.1	s__Thermovenabulum gondwanense	78.9937	53	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__Thermovenabulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124715.1	s__Thermosediminibacter litoriperuensis	78.6722	235	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__Thermosediminibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144645.1	s__Thermosediminibacter oceani	78.5735	230	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Thermosediminibacteraceae;g__Thermosediminibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840135.1	s__Biomaibacter sp012840135	76.7204	52	768	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Tepidanaerobacteraceae;g__Biomaibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:18,603] [INFO] GTDB search result was written to GCF_001562425.1_ASM156242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:18,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:18,605] [INFO] DFAST_QC result json was written to GCF_001562425.1_ASM156242v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:18,606] [INFO] DFAST_QC completed!
[2024-01-24 12:32:18,606] [INFO] Total running time: 0h0m45s