[2023-06-13 08:07:39,634] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:39,636] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:39,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference
[2023-06-13 08:07:40,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:40,867] [INFO] Task started: Prodigal
[2023-06-13 08:07:40,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg53dd8e94-0457-428d-9f03-17633b103a62/GCA_947458405.1_RE-18aug17-155_genomic.fna.gz | prodigal -d GCA_947458405.1_RE-18aug17-155_genomic.fna/cds.fna -a GCA_947458405.1_RE-18aug17-155_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:47,074] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:47,074] [INFO] Task started: HMMsearch
[2023-06-13 08:07:47,075] [INFO] Running command: hmmsearch --tblout GCA_947458405.1_RE-18aug17-155_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/reference_markers.hmm GCA_947458405.1_RE-18aug17-155_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:47,336] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:47,337] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53dd8e94-0457-428d-9f03-17633b103a62/GCA_947458405.1_RE-18aug17-155_genomic.fna.gz]
[2023-06-13 08:07:47,372] [INFO] Query marker FASTA was written to GCA_947458405.1_RE-18aug17-155_genomic.fna/markers.fasta
[2023-06-13 08:07:47,372] [INFO] Task started: Blastn
[2023-06-13 08:07:47,372] [INFO] Running command: blastn -query GCA_947458405.1_RE-18aug17-155_genomic.fna/markers.fasta -db /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/reference_markers.fasta -out GCA_947458405.1_RE-18aug17-155_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:47,926] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:47,932] [INFO] Selected 15 target genomes.
[2023-06-13 08:07:47,932] [INFO] Target genome list was writen to GCA_947458405.1_RE-18aug17-155_genomic.fna/target_genomes.txt
[2023-06-13 08:07:47,938] [INFO] Task started: fastANI
[2023-06-13 08:07:47,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg53dd8e94-0457-428d-9f03-17633b103a62/GCA_947458405.1_RE-18aug17-155_genomic.fna.gz --refList GCA_947458405.1_RE-18aug17-155_genomic.fna/target_genomes.txt --output GCA_947458405.1_RE-18aug17-155_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:52,610] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:52,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:52,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:52,614] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:07:52,614] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 08:07:52,614] [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
--------------------------------------------------------------------------------
[2023-06-13 08:07:52,616] [INFO] DFAST Taxonomy check result was written to GCA_947458405.1_RE-18aug17-155_genomic.fna/tc_result.tsv
[2023-06-13 08:07:52,617] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:52,618] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:52,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/checkm_data
[2023-06-13 08:07:52,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:52,670] [INFO] Task started: CheckM
[2023-06-13 08:07:52,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947458405.1_RE-18aug17-155_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947458405.1_RE-18aug17-155_genomic.fna/checkm_input GCA_947458405.1_RE-18aug17-155_genomic.fna/checkm_result
[2023-06-13 08:08:17,927] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:17,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:17,950] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:17,951] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:17,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947458405.1_RE-18aug17-155_genomic.fna/markers.fasta)
[2023-06-13 08:08:17,951] [INFO] Task started: Blastn
[2023-06-13 08:08:17,951] [INFO] Running command: blastn -query GCA_947458405.1_RE-18aug17-155_genomic.fna/markers.fasta -db /var/lib/cwl/stgd76131ac-61fa-4f89-96cb-590e2aeb9dc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_947458405.1_RE-18aug17-155_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:18,637] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:18,642] [INFO] Selected 19 target genomes.
[2023-06-13 08:08:18,642] [INFO] Target genome list was writen to GCA_947458405.1_RE-18aug17-155_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:18,657] [INFO] Task started: fastANI
[2023-06-13 08:08:18,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg53dd8e94-0457-428d-9f03-17633b103a62/GCA_947458405.1_RE-18aug17-155_genomic.fna.gz --refList GCA_947458405.1_RE-18aug17-155_genomic.fna/target_genomes_gtdb.txt --output GCA_947458405.1_RE-18aug17-155_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:26,181] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:26,186] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:08:26,187] [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_016711485.1	s__UBA2033 sp016711485	75.4646	71	1229	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:26,189] [INFO] GTDB search result was written to GCA_947458405.1_RE-18aug17-155_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:26,189] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:26,192] [INFO] DFAST_QC result json was written to GCA_947458405.1_RE-18aug17-155_genomic.fna/dqc_result.json
[2023-06-13 08:08:26,192] [INFO] DFAST_QC completed!
[2023-06-13 08:08:26,192] [INFO] Total running time: 0h0m47s