[2024-01-24 12:06:14,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference
[2024-01-24 12:06:15,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,930] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b5cf324-c5b7-4c36-889a-241dff833c10/GCF_900120375.1_PRJEB18029_genomic.fna.gz | prodigal -d GCF_900120375.1_PRJEB18029_genomic.fna/cds.fna -a GCF_900120375.1_PRJEB18029_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:21,898] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:21,899] [INFO] Task started: HMMsearch
[2024-01-24 12:06:21,899] [INFO] Running command: hmmsearch --tblout GCF_900120375.1_PRJEB18029_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/reference_markers.hmm GCF_900120375.1_PRJEB18029_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:22,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:22,132] [INFO] Found 6/6 markers.
[2024-01-24 12:06:22,152] [INFO] Query marker FASTA was written to GCF_900120375.1_PRJEB18029_genomic.fna/markers.fasta
[2024-01-24 12:06:22,152] [INFO] Task started: Blastn
[2024-01-24 12:06:22,152] [INFO] Running command: blastn -query GCF_900120375.1_PRJEB18029_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/reference_markers.fasta -out GCF_900120375.1_PRJEB18029_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:22,808] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:22,811] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:22,812] [INFO] Target genome list was writen to GCF_900120375.1_PRJEB18029_genomic.fna/target_genomes.txt
[2024-01-24 12:06:22,818] [INFO] Task started: fastANI
[2024-01-24 12:06:22,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5cf324-c5b7-4c36-889a-241dff833c10/GCF_900120375.1_PRJEB18029_genomic.fna.gz --refList GCF_900120375.1_PRJEB18029_genomic.fna/target_genomes.txt --output GCF_900120375.1_PRJEB18029_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:29,914] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:29,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:29,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:29,918] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:29,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:29,919] [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
Ndongobacter massiliensis	strain=Marseille-P3170	GCA_900120375.1	1871025	1871025	type	True	100.0	621	621	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:06:29,920] [INFO] DFAST Taxonomy check result was written to GCF_900120375.1_PRJEB18029_genomic.fna/tc_result.tsv
[2024-01-24 12:06:29,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:29,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:29,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/checkm_data
[2024-01-24 12:06:29,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:29,953] [INFO] Task started: CheckM
[2024-01-24 12:06:29,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900120375.1_PRJEB18029_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900120375.1_PRJEB18029_genomic.fna/checkm_input GCF_900120375.1_PRJEB18029_genomic.fna/checkm_result
[2024-01-24 12:06:53,063] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:53,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,165] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:53,166] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:53,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900120375.1_PRJEB18029_genomic.fna/markers.fasta)
[2024-01-24 12:06:53,166] [INFO] Task started: Blastn
[2024-01-24 12:06:53,167] [INFO] Running command: blastn -query GCF_900120375.1_PRJEB18029_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40ae1fe-685c-41cc-af8c-f38ed0d4da6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900120375.1_PRJEB18029_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:54,111] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:54,116] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:54,116] [INFO] Target genome list was writen to GCF_900120375.1_PRJEB18029_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:54,159] [INFO] Task started: fastANI
[2024-01-24 12:06:54,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5cf324-c5b7-4c36-889a-241dff833c10/GCF_900120375.1_PRJEB18029_genomic.fna.gz --refList GCF_900120375.1_PRJEB18029_genomic.fna/target_genomes_gtdb.txt --output GCF_900120375.1_PRJEB18029_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:03,101] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:03,105] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:03,105] [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_900120375.1	s__Ndongobacter massiliensis	100.0	621	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Ndongobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119705.1	s__Murdochiella vaginalis	83.758	56	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Murdochiella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:03,107] [INFO] GTDB search result was written to GCF_900120375.1_PRJEB18029_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:03,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:03,111] [INFO] DFAST_QC result json was written to GCF_900120375.1_PRJEB18029_genomic.fna/dqc_result.json
[2024-01-24 12:07:03,112] [INFO] DFAST_QC completed!
[2024-01-24 12:07:03,112] [INFO] Total running time: 0h0m49s