[2023-06-28 09:02:36,364] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:02:36,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:02:36,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference
[2023-06-28 09:02:37,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:02:37,563] [INFO] Task started: Prodigal
[2023-06-28 09:02:37,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgca984c22-ff09-4812-8fe0-4dca1451d26d/GCA_017521085.1_ASM1752108v1_genomic.fna.gz | prodigal -d GCA_017521085.1_ASM1752108v1_genomic.fna/cds.fna -a GCA_017521085.1_ASM1752108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:02:39,700] [INFO] Task succeeded: Prodigal
[2023-06-28 09:02:39,701] [INFO] Task started: HMMsearch
[2023-06-28 09:02:39,701] [INFO] Running command: hmmsearch --tblout GCA_017521085.1_ASM1752108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/reference_markers.hmm GCA_017521085.1_ASM1752108v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:02:39,863] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:02:39,864] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgca984c22-ff09-4812-8fe0-4dca1451d26d/GCA_017521085.1_ASM1752108v1_genomic.fna.gz]
[2023-06-28 09:02:39,880] [INFO] Query marker FASTA was written to GCA_017521085.1_ASM1752108v1_genomic.fna/markers.fasta
[2023-06-28 09:02:39,881] [INFO] Task started: Blastn
[2023-06-28 09:02:39,881] [INFO] Running command: blastn -query GCA_017521085.1_ASM1752108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/reference_markers.fasta -out GCA_017521085.1_ASM1752108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:02:40,383] [INFO] Task succeeded: Blastn
[2023-06-28 09:02:40,389] [INFO] Selected 14 target genomes.
[2023-06-28 09:02:40,389] [INFO] Target genome list was writen to GCA_017521085.1_ASM1752108v1_genomic.fna/target_genomes.txt
[2023-06-28 09:02:40,393] [INFO] Task started: fastANI
[2023-06-28 09:02:40,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgca984c22-ff09-4812-8fe0-4dca1451d26d/GCA_017521085.1_ASM1752108v1_genomic.fna.gz --refList GCA_017521085.1_ASM1752108v1_genomic.fna/target_genomes.txt --output GCA_017521085.1_ASM1752108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:02:47,867] [INFO] Task succeeded: fastANI
[2023-06-28 09:02:47,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:02:47,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:02:47,870] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:02:47,870] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:02:47,871] [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 09:02:47,877] [INFO] DFAST Taxonomy check result was written to GCA_017521085.1_ASM1752108v1_genomic.fna/tc_result.tsv
[2023-06-28 09:02:47,878] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:02:47,878] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:02:47,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/checkm_data
[2023-06-28 09:02:47,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:02:47,916] [INFO] Task started: CheckM
[2023-06-28 09:02:47,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017521085.1_ASM1752108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017521085.1_ASM1752108v1_genomic.fna/checkm_input GCA_017521085.1_ASM1752108v1_genomic.fna/checkm_result
[2023-06-28 09:03:01,961] [INFO] Task succeeded: CheckM
[2023-06-28 09:03:01,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.15%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:03:01,985] [INFO] ===== Completeness check finished =====
[2023-06-28 09:03:01,986] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:03:01,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017521085.1_ASM1752108v1_genomic.fna/markers.fasta)
[2023-06-28 09:03:01,987] [INFO] Task started: Blastn
[2023-06-28 09:03:01,987] [INFO] Running command: blastn -query GCA_017521085.1_ASM1752108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8adba516-d4ca-4ea9-9b74-b1217a437e02/dqc_reference/reference_markers_gtdb.fasta -out GCA_017521085.1_ASM1752108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:02,468] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:02,473] [INFO] Selected 13 target genomes.
[2023-06-28 09:03:02,473] [INFO] Target genome list was writen to GCA_017521085.1_ASM1752108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:03:02,492] [INFO] Task started: fastANI
[2023-06-28 09:03:02,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgca984c22-ff09-4812-8fe0-4dca1451d26d/GCA_017521085.1_ASM1752108v1_genomic.fna.gz --refList GCA_017521085.1_ASM1752108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017521085.1_ASM1752108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:03:06,775] [INFO] Task succeeded: fastANI
[2023-06-28 09:03:06,782] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 09:03:06,782] [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_017522015.1	s__SIG483 sp017522015	98.594	173	185	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__SIG483	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015068035.1	s__SIG483 sp015068035	94.4349	167	185	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__SIG483	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 09:03:06,784] [INFO] GTDB search result was written to GCA_017521085.1_ASM1752108v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:03:06,785] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:03:06,787] [INFO] DFAST_QC result json was written to GCA_017521085.1_ASM1752108v1_genomic.fna/dqc_result.json
[2023-06-28 09:03:06,787] [INFO] DFAST_QC completed!
[2023-06-28 09:03:06,787] [INFO] Total running time: 0h0m30s