[2023-06-28 06:40:09,950] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:40:09,958] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:40:09,958] [INFO] DQC Reference Directory: /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference
[2023-06-28 06:40:11,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:40:11,250] [INFO] Task started: Prodigal
[2023-06-28 06:40:11,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ed7e7ef-9ffb-49b9-ab61-40be3e10e21c/GCA_019310745.1_ASM1931074v1_genomic.fna.gz | prodigal -d GCA_019310745.1_ASM1931074v1_genomic.fna/cds.fna -a GCA_019310745.1_ASM1931074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:40:14,139] [INFO] Task succeeded: Prodigal
[2023-06-28 06:40:14,140] [INFO] Task started: HMMsearch
[2023-06-28 06:40:14,140] [INFO] Running command: hmmsearch --tblout GCA_019310745.1_ASM1931074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/reference_markers.hmm GCA_019310745.1_ASM1931074v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:40:14,369] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:40:14,371] [INFO] Found 6/6 markers.
[2023-06-28 06:40:14,391] [INFO] Query marker FASTA was written to GCA_019310745.1_ASM1931074v1_genomic.fna/markers.fasta
[2023-06-28 06:40:14,392] [INFO] Task started: Blastn
[2023-06-28 06:40:14,392] [INFO] Running command: blastn -query GCA_019310745.1_ASM1931074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/reference_markers.fasta -out GCA_019310745.1_ASM1931074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:14,875] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:14,879] [INFO] Selected 3 target genomes.
[2023-06-28 06:40:14,880] [INFO] Target genome list was writen to GCA_019310745.1_ASM1931074v1_genomic.fna/target_genomes.txt
[2023-06-28 06:40:14,881] [INFO] Task started: fastANI
[2023-06-28 06:40:14,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed7e7ef-9ffb-49b9-ab61-40be3e10e21c/GCA_019310745.1_ASM1931074v1_genomic.fna.gz --refList GCA_019310745.1_ASM1931074v1_genomic.fna/target_genomes.txt --output GCA_019310745.1_ASM1931074v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:40:16,452] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:16,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:40:16,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:40:16,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:40:16,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:40:16,454] [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 06:40:16,456] [INFO] DFAST Taxonomy check result was written to GCA_019310745.1_ASM1931074v1_genomic.fna/tc_result.tsv
[2023-06-28 06:40:16,456] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:40:16,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:40:16,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/checkm_data
[2023-06-28 06:40:16,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:40:16,482] [INFO] Task started: CheckM
[2023-06-28 06:40:16,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310745.1_ASM1931074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310745.1_ASM1931074v1_genomic.fna/checkm_input GCA_019310745.1_ASM1931074v1_genomic.fna/checkm_result
[2023-06-28 06:40:33,179] [INFO] Task succeeded: CheckM
[2023-06-28 06:40:33,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.98%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:40:33,207] [INFO] ===== Completeness check finished =====
[2023-06-28 06:40:33,207] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:40:33,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310745.1_ASM1931074v1_genomic.fna/markers.fasta)
[2023-06-28 06:40:33,208] [INFO] Task started: Blastn
[2023-06-28 06:40:33,208] [INFO] Running command: blastn -query GCA_019310745.1_ASM1931074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529af9d-88ab-4bec-8a54-365c6d39b016/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310745.1_ASM1931074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:33,700] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:33,703] [INFO] Selected 15 target genomes.
[2023-06-28 06:40:33,704] [INFO] Target genome list was writen to GCA_019310745.1_ASM1931074v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:40:33,714] [INFO] Task started: fastANI
[2023-06-28 06:40:33,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed7e7ef-9ffb-49b9-ab61-40be3e10e21c/GCA_019310745.1_ASM1931074v1_genomic.fna.gz --refList GCA_019310745.1_ASM1931074v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310745.1_ASM1931074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:40:40,026] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:40,033] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:40:40,033] [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_003646875.1	s__B33-G16 sp003646875	87.1402	179	359	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	98.46	98.46	0.69	0.69	2	-
GCA_013375385.1	s__B33-G16 sp013375385	77.8536	82	359	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:40:40,035] [INFO] GTDB search result was written to GCA_019310745.1_ASM1931074v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:40:40,036] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:40:40,039] [INFO] DFAST_QC result json was written to GCA_019310745.1_ASM1931074v1_genomic.fna/dqc_result.json
[2023-06-28 06:40:40,039] [INFO] DFAST_QC completed!
[2023-06-28 06:40:40,039] [INFO] Total running time: 0h0m30s