[2024-01-24 11:35:23,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f0924d9-0db4-4bc1-befd-ab84b6d08059/GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna.gz | prodigal -d GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/cds.fna -a GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,762] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,762] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,763] [INFO] Running command: hmmsearch --tblout GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/reference_markers.hmm GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:32,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:32,033] [INFO] Found 6/6 markers.
[2024-01-24 11:35:32,056] [INFO] Query marker FASTA was written to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/markers.fasta
[2024-01-24 11:35:32,056] [INFO] Task started: Blastn
[2024-01-24 11:35:32,057] [INFO] Running command: blastn -query GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/markers.fasta -db /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/reference_markers.fasta -out GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,008] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:33,008] [INFO] Target genome list was writen to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,037] [INFO] Task started: fastANI
[2024-01-24 11:35:33,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0924d9-0db4-4bc1-befd-ab84b6d08059/GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna.gz --refList GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/target_genomes.txt --output GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:41,316] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:41,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:41,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:41,319] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:41,319] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 11:35:41,319] [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
--------------------------------------------------------------------------------
[2024-01-24 11:35:41,321] [INFO] DFAST Taxonomy check result was written to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/tc_result.tsv
[2024-01-24 11:35:41,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:41,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:41,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/checkm_data
[2024-01-24 11:35:41,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:41,346] [INFO] Task started: CheckM
[2024-01-24 11:35:41,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/checkm_input GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/checkm_result
[2024-01-24 11:36:03,512] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:03,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:03,533] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:03,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:03,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/markers.fasta)
[2024-01-24 11:36:03,534] [INFO] Task started: Blastn
[2024-01-24 11:36:03,534] [INFO] Running command: blastn -query GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/markers.fasta -db /var/lib/cwl/stg85f661f8-6057-4da8-af3d-18ea61884ae1/dqc_reference/reference_markers_gtdb.fasta -out GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:04,654] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:04,658] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:04,659] [INFO] Target genome list was writen to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:04,671] [INFO] Task started: fastANI
[2024-01-24 11:36:04,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0924d9-0db4-4bc1-befd-ab84b6d08059/GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna.gz --refList GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/target_genomes_gtdb.txt --output GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,115] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,125] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,125] [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_910588305.1	s__MGBC100320 sp910588305	98.124	561	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910577945.1	s__MGBC100320 sp910577945	78.9609	244	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579205.1	s__MGBC100320 sp910579205	78.8213	198	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799665.1	s__MGBC100320 sp014799665	78.638	215	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586925.1	s__MGBC100320 sp910586925	78.5821	209	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578545.1	s__MGBC100320 sp910578545	78.5338	184	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585055.1	s__MGBC100320 sp910585055	78.1549	160	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588315.1	s__MGBC100320 sp910588315	78.1185	154	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577995.1	s__MGBC100320 sp910577995	78.0537	174	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587455.1	s__MGBC100320 sp910587455	77.8733	205	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__MGBC100320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:09,126] [INFO] GTDB search result was written to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:09,129] [INFO] DFAST_QC result json was written to GCF_943192945.1_Eubacteriales_fam_nov_CLA_AA_M11_genomic.fna/dqc_result.json
[2024-01-24 11:36:09,130] [INFO] DFAST_QC completed!
[2024-01-24 11:36:09,130] [INFO] Total running time: 0h0m46s