[2023-06-28 10:47:17,201] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:47:17,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:47:17,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference
[2023-06-28 10:47:19,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:47:19,439] [INFO] Task started: Prodigal
[2023-06-28 10:47:19,439] [INFO] Running command: gunzip -c /var/lib/cwl/stgad944eb7-8ec6-4dfe-b276-136074114d61/GCA_015521005.1_ASM1552100v1_genomic.fna.gz | prodigal -d GCA_015521005.1_ASM1552100v1_genomic.fna/cds.fna -a GCA_015521005.1_ASM1552100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:47:25,687] [INFO] Task succeeded: Prodigal
[2023-06-28 10:47:25,688] [INFO] Task started: HMMsearch
[2023-06-28 10:47:25,688] [INFO] Running command: hmmsearch --tblout GCA_015521005.1_ASM1552100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/reference_markers.hmm GCA_015521005.1_ASM1552100v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:47:25,884] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:47:25,886] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgad944eb7-8ec6-4dfe-b276-136074114d61/GCA_015521005.1_ASM1552100v1_genomic.fna.gz]
[2023-06-28 10:47:25,909] [INFO] Query marker FASTA was written to GCA_015521005.1_ASM1552100v1_genomic.fna/markers.fasta
[2023-06-28 10:47:25,909] [INFO] Task started: Blastn
[2023-06-28 10:47:25,909] [INFO] Running command: blastn -query GCA_015521005.1_ASM1552100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/reference_markers.fasta -out GCA_015521005.1_ASM1552100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:26,383] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:26,387] [INFO] Selected 6 target genomes.
[2023-06-28 10:47:26,388] [INFO] Target genome list was writen to GCA_015521005.1_ASM1552100v1_genomic.fna/target_genomes.txt
[2023-06-28 10:47:26,391] [INFO] Task started: fastANI
[2023-06-28 10:47:26,391] [INFO] Running command: fastANI --query /var/lib/cwl/stgad944eb7-8ec6-4dfe-b276-136074114d61/GCA_015521005.1_ASM1552100v1_genomic.fna.gz --refList GCA_015521005.1_ASM1552100v1_genomic.fna/target_genomes.txt --output GCA_015521005.1_ASM1552100v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:47:28,751] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:28,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:47:28,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:47:28,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:47:28,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:47:28,755] [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
--------------------------------------------------------------------------------
[2023-06-28 10:47:28,757] [INFO] DFAST Taxonomy check result was written to GCA_015521005.1_ASM1552100v1_genomic.fna/tc_result.tsv
[2023-06-28 10:47:28,758] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:47:28,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:47:28,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/checkm_data
[2023-06-28 10:47:28,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:47:28,788] [INFO] Task started: CheckM
[2023-06-28 10:47:28,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015521005.1_ASM1552100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015521005.1_ASM1552100v1_genomic.fna/checkm_input GCA_015521005.1_ASM1552100v1_genomic.fna/checkm_result
[2023-06-28 10:47:53,583] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:53,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:53,606] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:53,606] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:53,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015521005.1_ASM1552100v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:53,607] [INFO] Task started: Blastn
[2023-06-28 10:47:53,607] [INFO] Running command: blastn -query GCA_015521005.1_ASM1552100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac40c127-6794-4d85-b19d-56a965b85f84/dqc_reference/reference_markers_gtdb.fasta -out GCA_015521005.1_ASM1552100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:54,038] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:54,042] [INFO] Selected 7 target genomes.
[2023-06-28 10:47:54,042] [INFO] Target genome list was writen to GCA_015521005.1_ASM1552100v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:54,046] [INFO] Task started: fastANI
[2023-06-28 10:47:54,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgad944eb7-8ec6-4dfe-b276-136074114d61/GCA_015521005.1_ASM1552100v1_genomic.fna.gz --refList GCA_015521005.1_ASM1552100v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015521005.1_ASM1552100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:47:56,109] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:56,114] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:47:56,114] [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_015520485.1	s__Archaeoglobus_C sp015520485	99.4109	455	502	d__Archaea;p__Halobacteriota;c__Archaeoglobi;o__Archaeoglobales;f__Archaeoglobaceae;g__Archaeoglobus_C	95.0	99.53	99.41	0.96	0.93	6	conclusive
--------------------------------------------------------------------------------
[2023-06-28 10:47:56,116] [INFO] GTDB search result was written to GCA_015521005.1_ASM1552100v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:47:56,117] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:47:56,119] [INFO] DFAST_QC result json was written to GCA_015521005.1_ASM1552100v1_genomic.fna/dqc_result.json
[2023-06-28 10:47:56,119] [INFO] DFAST_QC completed!
[2023-06-28 10:47:56,119] [INFO] Total running time: 0h0m39s