[2023-06-28 19:48:07,219] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:07,223] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:07,224] [INFO] DQC Reference Directory: /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference
[2023-06-28 19:48:08,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:08,522] [INFO] Task started: Prodigal
[2023-06-28 19:48:08,522] [INFO] Running command: gunzip -c /var/lib/cwl/stgf12d0905-c6b8-4bdb-8dc1-133d2c268ec8/GCA_017397075.1_ASM1739707v1_genomic.fna.gz | prodigal -d GCA_017397075.1_ASM1739707v1_genomic.fna/cds.fna -a GCA_017397075.1_ASM1739707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:13,414] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:13,414] [INFO] Task started: HMMsearch
[2023-06-28 19:48:13,415] [INFO] Running command: hmmsearch --tblout GCA_017397075.1_ASM1739707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/reference_markers.hmm GCA_017397075.1_ASM1739707v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:13,642] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:13,644] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf12d0905-c6b8-4bdb-8dc1-133d2c268ec8/GCA_017397075.1_ASM1739707v1_genomic.fna.gz]
[2023-06-28 19:48:13,665] [INFO] Query marker FASTA was written to GCA_017397075.1_ASM1739707v1_genomic.fna/markers.fasta
[2023-06-28 19:48:13,665] [INFO] Task started: Blastn
[2023-06-28 19:48:13,665] [INFO] Running command: blastn -query GCA_017397075.1_ASM1739707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/reference_markers.fasta -out GCA_017397075.1_ASM1739707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:14,255] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:14,259] [INFO] Selected 20 target genomes.
[2023-06-28 19:48:14,259] [INFO] Target genome list was writen to GCA_017397075.1_ASM1739707v1_genomic.fna/target_genomes.txt
[2023-06-28 19:48:14,265] [INFO] Task started: fastANI
[2023-06-28 19:48:14,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12d0905-c6b8-4bdb-8dc1-133d2c268ec8/GCA_017397075.1_ASM1739707v1_genomic.fna.gz --refList GCA_017397075.1_ASM1739707v1_genomic.fna/target_genomes.txt --output GCA_017397075.1_ASM1739707v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:28,352] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:28,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:28,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:28,355] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:28,355] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:48:28,355] [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 19:48:28,357] [INFO] DFAST Taxonomy check result was written to GCA_017397075.1_ASM1739707v1_genomic.fna/tc_result.tsv
[2023-06-28 19:48:28,358] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:28,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:28,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/checkm_data
[2023-06-28 19:48:28,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:28,389] [INFO] Task started: CheckM
[2023-06-28 19:48:28,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017397075.1_ASM1739707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017397075.1_ASM1739707v1_genomic.fna/checkm_input GCA_017397075.1_ASM1739707v1_genomic.fna/checkm_result
[2023-06-28 19:48:49,579] [INFO] Task succeeded: CheckM
[2023-06-28 19:48:49,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:48:49,599] [INFO] ===== Completeness check finished =====
[2023-06-28 19:48:49,600] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:48:49,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017397075.1_ASM1739707v1_genomic.fna/markers.fasta)
[2023-06-28 19:48:49,600] [INFO] Task started: Blastn
[2023-06-28 19:48:49,601] [INFO] Running command: blastn -query GCA_017397075.1_ASM1739707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb175bf1d-815d-4adf-b790-bc5e2a5517d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_017397075.1_ASM1739707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:50,533] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:50,539] [INFO] Selected 22 target genomes.
[2023-06-28 19:48:50,539] [INFO] Target genome list was writen to GCA_017397075.1_ASM1739707v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:48:50,552] [INFO] Task started: fastANI
[2023-06-28 19:48:50,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12d0905-c6b8-4bdb-8dc1-133d2c268ec8/GCA_017397075.1_ASM1739707v1_genomic.fna.gz --refList GCA_017397075.1_ASM1739707v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017397075.1_ASM1739707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:48:58,453] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:58,458] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:48:58,459] [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_017397075.1	s__RGIG1893 sp017397075	100.0	498	501	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG1893	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-28 19:48:58,461] [INFO] GTDB search result was written to GCA_017397075.1_ASM1739707v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:48:58,462] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:48:58,464] [INFO] DFAST_QC result json was written to GCA_017397075.1_ASM1739707v1_genomic.fna/dqc_result.json
[2023-06-28 19:48:58,465] [INFO] DFAST_QC completed!
[2023-06-28 19:48:58,465] [INFO] Total running time: 0h0m51s