[2023-06-28 16:53:01,297] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:53:01,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:53:01,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference
[2023-06-28 16:53:02,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:53:02,473] [INFO] Task started: Prodigal
[2023-06-28 16:53:02,474] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc6420e-19de-4216-bf66-f41bcde530fa/GCA_017889545.1_ASM1788954v1_genomic.fna.gz | prodigal -d GCA_017889545.1_ASM1788954v1_genomic.fna/cds.fna -a GCA_017889545.1_ASM1788954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:53:10,977] [INFO] Task succeeded: Prodigal
[2023-06-28 16:53:10,977] [INFO] Task started: HMMsearch
[2023-06-28 16:53:10,977] [INFO] Running command: hmmsearch --tblout GCA_017889545.1_ASM1788954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/reference_markers.hmm GCA_017889545.1_ASM1788954v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:53:11,206] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:53:11,207] [INFO] Found 6/6 markers.
[2023-06-28 16:53:11,235] [INFO] Query marker FASTA was written to GCA_017889545.1_ASM1788954v1_genomic.fna/markers.fasta
[2023-06-28 16:53:11,236] [INFO] Task started: Blastn
[2023-06-28 16:53:11,236] [INFO] Running command: blastn -query GCA_017889545.1_ASM1788954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/reference_markers.fasta -out GCA_017889545.1_ASM1788954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:53:11,814] [INFO] Task succeeded: Blastn
[2023-06-28 16:53:11,818] [INFO] Selected 15 target genomes.
[2023-06-28 16:53:11,818] [INFO] Target genome list was writen to GCA_017889545.1_ASM1788954v1_genomic.fna/target_genomes.txt
[2023-06-28 16:53:11,820] [INFO] Task started: fastANI
[2023-06-28 16:53:11,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc6420e-19de-4216-bf66-f41bcde530fa/GCA_017889545.1_ASM1788954v1_genomic.fna.gz --refList GCA_017889545.1_ASM1788954v1_genomic.fna/target_genomes.txt --output GCA_017889545.1_ASM1788954v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:53:21,338] [INFO] Task succeeded: fastANI
[2023-06-28 16:53:21,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:53:21,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:53:21,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:53:21,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:53:21,341] [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 16:53:21,343] [INFO] DFAST Taxonomy check result was written to GCA_017889545.1_ASM1788954v1_genomic.fna/tc_result.tsv
[2023-06-28 16:53:21,344] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:53:21,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:53:21,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/checkm_data
[2023-06-28 16:53:21,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:53:21,382] [INFO] Task started: CheckM
[2023-06-28 16:53:21,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017889545.1_ASM1788954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017889545.1_ASM1788954v1_genomic.fna/checkm_input GCA_017889545.1_ASM1788954v1_genomic.fna/checkm_result
[2023-06-28 16:53:51,138] [INFO] Task succeeded: CheckM
[2023-06-28 16:53:51,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:53:51,156] [INFO] ===== Completeness check finished =====
[2023-06-28 16:53:51,156] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:53:51,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017889545.1_ASM1788954v1_genomic.fna/markers.fasta)
[2023-06-28 16:53:51,157] [INFO] Task started: Blastn
[2023-06-28 16:53:51,157] [INFO] Running command: blastn -query GCA_017889545.1_ASM1788954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ce8a89-83c9-4443-a027-52ab20dce451/dqc_reference/reference_markers_gtdb.fasta -out GCA_017889545.1_ASM1788954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:53:51,956] [INFO] Task succeeded: Blastn
[2023-06-28 16:53:51,960] [INFO] Selected 24 target genomes.
[2023-06-28 16:53:51,960] [INFO] Target genome list was writen to GCA_017889545.1_ASM1788954v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:53:51,967] [INFO] Task started: fastANI
[2023-06-28 16:53:51,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc6420e-19de-4216-bf66-f41bcde530fa/GCA_017889545.1_ASM1788954v1_genomic.fna.gz --refList GCA_017889545.1_ASM1788954v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017889545.1_ASM1788954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:54:04,167] [INFO] Task succeeded: fastANI
[2023-06-28 16:54:04,171] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:54:04,171] [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_017889545.1	s__CTSoil-072 sp017889545	100.0	1062	1063	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__CTSoil-072;f__CTSoil-072;g__CTSoil-072	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017861495.1	s__CTSoil-072 sp017861495	78.5954	310	1063	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__CTSoil-072;f__CTSoil-072;g__CTSoil-072	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:54:04,173] [INFO] GTDB search result was written to GCA_017889545.1_ASM1788954v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:54:04,174] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:54:04,177] [INFO] DFAST_QC result json was written to GCA_017889545.1_ASM1788954v1_genomic.fna/dqc_result.json
[2023-06-28 16:54:04,177] [INFO] DFAST_QC completed!
[2023-06-28 16:54:04,177] [INFO] Total running time: 0h1m3s