[2023-06-27 22:54:07,766] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:54:07,768] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:54:07,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference
[2023-06-27 22:54:09,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:54:09,062] [INFO] Task started: Prodigal
[2023-06-27 22:54:09,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg969231f5-0a6a-47ca-89e3-82e0dcd56e24/GCA_026989045.1_ASM2698904v1_genomic.fna.gz | prodigal -d GCA_026989045.1_ASM2698904v1_genomic.fna/cds.fna -a GCA_026989045.1_ASM2698904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:54:13,182] [INFO] Task succeeded: Prodigal
[2023-06-27 22:54:13,183] [INFO] Task started: HMMsearch
[2023-06-27 22:54:13,183] [INFO] Running command: hmmsearch --tblout GCA_026989045.1_ASM2698904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/reference_markers.hmm GCA_026989045.1_ASM2698904v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:54:13,432] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:54:13,433] [INFO] Found 6/6 markers.
[2023-06-27 22:54:13,457] [INFO] Query marker FASTA was written to GCA_026989045.1_ASM2698904v1_genomic.fna/markers.fasta
[2023-06-27 22:54:13,457] [INFO] Task started: Blastn
[2023-06-27 22:54:13,457] [INFO] Running command: blastn -query GCA_026989045.1_ASM2698904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/reference_markers.fasta -out GCA_026989045.1_ASM2698904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:14,026] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:14,032] [INFO] Selected 32 target genomes.
[2023-06-27 22:54:14,032] [INFO] Target genome list was writen to GCA_026989045.1_ASM2698904v1_genomic.fna/target_genomes.txt
[2023-06-27 22:54:14,077] [INFO] Task started: fastANI
[2023-06-27 22:54:14,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg969231f5-0a6a-47ca-89e3-82e0dcd56e24/GCA_026989045.1_ASM2698904v1_genomic.fna.gz --refList GCA_026989045.1_ASM2698904v1_genomic.fna/target_genomes.txt --output GCA_026989045.1_ASM2698904v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:54:30,905] [INFO] Task succeeded: fastANI
[2023-06-27 22:54:30,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:54:30,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:54:30,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:54:30,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 22:54:30,908] [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
--------------------------------------------------------------------------------
[2023-06-27 22:54:30,910] [INFO] DFAST Taxonomy check result was written to GCA_026989045.1_ASM2698904v1_genomic.fna/tc_result.tsv
[2023-06-27 22:54:30,911] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:54:30,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:54:30,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/checkm_data
[2023-06-27 22:54:30,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:54:30,947] [INFO] Task started: CheckM
[2023-06-27 22:54:30,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026989045.1_ASM2698904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026989045.1_ASM2698904v1_genomic.fna/checkm_input GCA_026989045.1_ASM2698904v1_genomic.fna/checkm_result
[2023-06-27 22:54:50,603] [INFO] Task succeeded: CheckM
[2023-06-27 22:54:50,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:54:50,627] [INFO] ===== Completeness check finished =====
[2023-06-27 22:54:50,627] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:54:50,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026989045.1_ASM2698904v1_genomic.fna/markers.fasta)
[2023-06-27 22:54:50,628] [INFO] Task started: Blastn
[2023-06-27 22:54:50,628] [INFO] Running command: blastn -query GCA_026989045.1_ASM2698904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b12dde8-8c0d-452b-8c70-240ef26b462a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026989045.1_ASM2698904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:51,392] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:51,404] [INFO] Selected 36 target genomes.
[2023-06-27 22:54:51,405] [INFO] Target genome list was writen to GCA_026989045.1_ASM2698904v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:54:51,438] [INFO] Task started: fastANI
[2023-06-27 22:54:51,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg969231f5-0a6a-47ca-89e3-82e0dcd56e24/GCA_026989045.1_ASM2698904v1_genomic.fna.gz --refList GCA_026989045.1_ASM2698904v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026989045.1_ASM2698904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:55:05,171] [INFO] Task succeeded: fastANI
[2023-06-27 22:55:05,175] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:55:05,176] [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_015490455.1	s__S141-66 sp015490455	76.4382	93	589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__S141-66	95.0	99.81	99.81	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-27 22:55:05,178] [INFO] GTDB search result was written to GCA_026989045.1_ASM2698904v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:55:05,179] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:55:05,181] [INFO] DFAST_QC result json was written to GCA_026989045.1_ASM2698904v1_genomic.fna/dqc_result.json
[2023-06-27 22:55:05,181] [INFO] DFAST_QC completed!
[2023-06-27 22:55:05,181] [INFO] Total running time: 0h0m57s