[2023-06-29 14:46:18,351] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:46:18,354] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:46:18,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference
[2023-06-29 14:46:19,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:46:19,845] [INFO] Task started: Prodigal
[2023-06-29 14:46:19,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2c0490f-ab6a-4b2c-9244-71b39b0bac88/GCA_021286925.1_ASM2128692v1_genomic.fna.gz | prodigal -d GCA_021286925.1_ASM2128692v1_genomic.fna/cds.fna -a GCA_021286925.1_ASM2128692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:46:24,966] [INFO] Task succeeded: Prodigal
[2023-06-29 14:46:24,966] [INFO] Task started: HMMsearch
[2023-06-29 14:46:24,966] [INFO] Running command: hmmsearch --tblout GCA_021286925.1_ASM2128692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/reference_markers.hmm GCA_021286925.1_ASM2128692v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:46:25,236] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:46:25,237] [INFO] Found 6/6 markers.
[2023-06-29 14:46:25,263] [INFO] Query marker FASTA was written to GCA_021286925.1_ASM2128692v1_genomic.fna/markers.fasta
[2023-06-29 14:46:25,264] [INFO] Task started: Blastn
[2023-06-29 14:46:25,264] [INFO] Running command: blastn -query GCA_021286925.1_ASM2128692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/reference_markers.fasta -out GCA_021286925.1_ASM2128692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:46:25,936] [INFO] Task succeeded: Blastn
[2023-06-29 14:46:25,943] [INFO] Selected 17 target genomes.
[2023-06-29 14:46:25,944] [INFO] Target genome list was writen to GCA_021286925.1_ASM2128692v1_genomic.fna/target_genomes.txt
[2023-06-29 14:46:25,945] [INFO] Task started: fastANI
[2023-06-29 14:46:25,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c0490f-ab6a-4b2c-9244-71b39b0bac88/GCA_021286925.1_ASM2128692v1_genomic.fna.gz --refList GCA_021286925.1_ASM2128692v1_genomic.fna/target_genomes.txt --output GCA_021286925.1_ASM2128692v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:46:38,270] [INFO] Task succeeded: fastANI
[2023-06-29 14:46:38,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:46:38,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:46:38,272] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:46:38,272] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:46:38,272] [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
--------------------------------------------------------------------------------
[2023-06-29 14:46:38,274] [INFO] DFAST Taxonomy check result was written to GCA_021286925.1_ASM2128692v1_genomic.fna/tc_result.tsv
[2023-06-29 14:46:38,275] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:46:38,275] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:46:38,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/checkm_data
[2023-06-29 14:46:38,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:46:38,310] [INFO] Task started: CheckM
[2023-06-29 14:46:38,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021286925.1_ASM2128692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021286925.1_ASM2128692v1_genomic.fna/checkm_input GCA_021286925.1_ASM2128692v1_genomic.fna/checkm_result
[2023-06-29 14:47:00,292] [INFO] Task succeeded: CheckM
[2023-06-29 14:47:00,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:47:00,313] [INFO] ===== Completeness check finished =====
[2023-06-29 14:47:00,314] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:47:00,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021286925.1_ASM2128692v1_genomic.fna/markers.fasta)
[2023-06-29 14:47:00,315] [INFO] Task started: Blastn
[2023-06-29 14:47:00,315] [INFO] Running command: blastn -query GCA_021286925.1_ASM2128692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg651231ec-20fd-4f0d-af91-9ab514e25655/dqc_reference/reference_markers_gtdb.fasta -out GCA_021286925.1_ASM2128692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:47:01,144] [INFO] Task succeeded: Blastn
[2023-06-29 14:47:01,148] [INFO] Selected 28 target genomes.
[2023-06-29 14:47:01,149] [INFO] Target genome list was writen to GCA_021286925.1_ASM2128692v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:47:01,186] [INFO] Task started: fastANI
[2023-06-29 14:47:01,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c0490f-ab6a-4b2c-9244-71b39b0bac88/GCA_021286925.1_ASM2128692v1_genomic.fna.gz --refList GCA_021286925.1_ASM2128692v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021286925.1_ASM2128692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:47:14,795] [INFO] Task succeeded: fastANI
[2023-06-29 14:47:14,800] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:47:14,801] [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_011368145.1	s__Rectinema sp011368145	77.2634	52	487	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__Rectinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:47:14,802] [INFO] GTDB search result was written to GCA_021286925.1_ASM2128692v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:47:14,803] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:47:14,805] [INFO] DFAST_QC result json was written to GCA_021286925.1_ASM2128692v1_genomic.fna/dqc_result.json
[2023-06-29 14:47:14,805] [INFO] DFAST_QC completed!
[2023-06-29 14:47:14,805] [INFO] Total running time: 0h0m56s