[2023-06-26 23:34:25,607] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:34:25,617] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:34:25,618] [INFO] DQC Reference Directory: /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference
[2023-06-26 23:34:26,989] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:34:26,990] [INFO] Task started: Prodigal
[2023-06-26 23:34:26,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f4e8faa-89f1-407e-971e-74331d2afa00/GCA_026391995.1_ASM2639199v1_genomic.fna.gz | prodigal -d GCA_026391995.1_ASM2639199v1_genomic.fna/cds.fna -a GCA_026391995.1_ASM2639199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:34:31,313] [INFO] Task succeeded: Prodigal
[2023-06-26 23:34:31,314] [INFO] Task started: HMMsearch
[2023-06-26 23:34:31,314] [INFO] Running command: hmmsearch --tblout GCA_026391995.1_ASM2639199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/reference_markers.hmm GCA_026391995.1_ASM2639199v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:34:31,561] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:34:31,562] [INFO] Found 6/6 markers.
[2023-06-26 23:34:31,584] [INFO] Query marker FASTA was written to GCA_026391995.1_ASM2639199v1_genomic.fna/markers.fasta
[2023-06-26 23:34:31,584] [INFO] Task started: Blastn
[2023-06-26 23:34:31,584] [INFO] Running command: blastn -query GCA_026391995.1_ASM2639199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/reference_markers.fasta -out GCA_026391995.1_ASM2639199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:34:32,187] [INFO] Task succeeded: Blastn
[2023-06-26 23:34:32,192] [INFO] Selected 25 target genomes.
[2023-06-26 23:34:32,193] [INFO] Target genome list was writen to GCA_026391995.1_ASM2639199v1_genomic.fna/target_genomes.txt
[2023-06-26 23:34:32,271] [INFO] Task started: fastANI
[2023-06-26 23:34:32,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4e8faa-89f1-407e-971e-74331d2afa00/GCA_026391995.1_ASM2639199v1_genomic.fna.gz --refList GCA_026391995.1_ASM2639199v1_genomic.fna/target_genomes.txt --output GCA_026391995.1_ASM2639199v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:34:50,379] [INFO] Task succeeded: fastANI
[2023-06-26 23:34:50,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:34:50,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:34:50,382] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:34:50,382] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 23:34:50,383] [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
--------------------------------------------------------------------------------
[2023-06-26 23:34:50,385] [INFO] DFAST Taxonomy check result was written to GCA_026391995.1_ASM2639199v1_genomic.fna/tc_result.tsv
[2023-06-26 23:34:50,385] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:34:50,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:34:50,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/checkm_data
[2023-06-26 23:34:50,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:34:50,416] [INFO] Task started: CheckM
[2023-06-26 23:34:50,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026391995.1_ASM2639199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026391995.1_ASM2639199v1_genomic.fna/checkm_input GCA_026391995.1_ASM2639199v1_genomic.fna/checkm_result
[2023-06-26 23:35:10,154] [INFO] Task succeeded: CheckM
[2023-06-26 23:35:10,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.36%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:35:10,177] [INFO] ===== Completeness check finished =====
[2023-06-26 23:35:10,177] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:35:10,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026391995.1_ASM2639199v1_genomic.fna/markers.fasta)
[2023-06-26 23:35:10,178] [INFO] Task started: Blastn
[2023-06-26 23:35:10,178] [INFO] Running command: blastn -query GCA_026391995.1_ASM2639199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93ef384-8072-4aa2-9de7-5f1ac416ba50/dqc_reference/reference_markers_gtdb.fasta -out GCA_026391995.1_ASM2639199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:35:11,060] [INFO] Task succeeded: Blastn
[2023-06-26 23:35:11,064] [INFO] Selected 22 target genomes.
[2023-06-26 23:35:11,064] [INFO] Target genome list was writen to GCA_026391995.1_ASM2639199v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:35:11,087] [INFO] Task started: fastANI
[2023-06-26 23:35:11,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4e8faa-89f1-407e-971e-74331d2afa00/GCA_026391995.1_ASM2639199v1_genomic.fna.gz --refList GCA_026391995.1_ASM2639199v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026391995.1_ASM2639199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:35:25,613] [INFO] Task succeeded: fastANI
[2023-06-26 23:35:25,618] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:35:25,618] [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_012729785.1	s__UBA1439 sp002329605	77.6818	108	390	d__Bacteria;p__UBA1439;c__UBA1439;o__UBA1439;f__UBA1439;g__UBA1439	95.0	99.84	99.84	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-26 23:35:25,621] [INFO] GTDB search result was written to GCA_026391995.1_ASM2639199v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:35:25,621] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:35:25,653] [INFO] DFAST_QC result json was written to GCA_026391995.1_ASM2639199v1_genomic.fna/dqc_result.json
[2023-06-26 23:35:25,653] [INFO] DFAST_QC completed!
[2023-06-26 23:35:25,654] [INFO] Total running time: 0h1m0s