[2023-06-27 17:41:04,869] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:04,884] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:04,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference
[2023-06-27 17:41:06,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:06,094] [INFO] Task started: Prodigal
[2023-06-27 17:41:06,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg27451a04-f8a2-4b63-83a8-a8e9bda8f859/GCA_026706695.1_ASM2670669v1_genomic.fna.gz | prodigal -d GCA_026706695.1_ASM2670669v1_genomic.fna/cds.fna -a GCA_026706695.1_ASM2670669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:10,022] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:10,023] [INFO] Task started: HMMsearch
[2023-06-27 17:41:10,023] [INFO] Running command: hmmsearch --tblout GCA_026706695.1_ASM2670669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/reference_markers.hmm GCA_026706695.1_ASM2670669v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:10,177] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:10,178] [INFO] Found 6/6 markers.
[2023-06-27 17:41:10,196] [INFO] Query marker FASTA was written to GCA_026706695.1_ASM2670669v1_genomic.fna/markers.fasta
[2023-06-27 17:41:10,197] [INFO] Task started: Blastn
[2023-06-27 17:41:10,197] [INFO] Running command: blastn -query GCA_026706695.1_ASM2670669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/reference_markers.fasta -out GCA_026706695.1_ASM2670669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:10,748] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:10,752] [INFO] Selected 19 target genomes.
[2023-06-27 17:41:10,752] [INFO] Target genome list was writen to GCA_026706695.1_ASM2670669v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:10,754] [INFO] Task started: fastANI
[2023-06-27 17:41:10,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg27451a04-f8a2-4b63-83a8-a8e9bda8f859/GCA_026706695.1_ASM2670669v1_genomic.fna.gz --refList GCA_026706695.1_ASM2670669v1_genomic.fna/target_genomes.txt --output GCA_026706695.1_ASM2670669v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:22,469] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:22,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:22,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:22,471] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:22,471] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:41:22,471] [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 17:41:22,473] [INFO] DFAST Taxonomy check result was written to GCA_026706695.1_ASM2670669v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:22,474] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:22,474] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:22,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/checkm_data
[2023-06-27 17:41:22,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:22,497] [INFO] Task started: CheckM
[2023-06-27 17:41:22,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706695.1_ASM2670669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706695.1_ASM2670669v1_genomic.fna/checkm_input GCA_026706695.1_ASM2670669v1_genomic.fna/checkm_result
[2023-06-27 17:41:40,621] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:40,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:40,643] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:40,644] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:40,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706695.1_ASM2670669v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:40,644] [INFO] Task started: Blastn
[2023-06-27 17:41:40,644] [INFO] Running command: blastn -query GCA_026706695.1_ASM2670669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05239176-969c-4793-a348-23be229f35bc/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706695.1_ASM2670669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:41,438] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:41,453] [INFO] Selected 11 target genomes.
[2023-06-27 17:41:41,453] [INFO] Target genome list was writen to GCA_026706695.1_ASM2670669v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:41:41,456] [INFO] Task started: fastANI
[2023-06-27 17:41:41,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg27451a04-f8a2-4b63-83a8-a8e9bda8f859/GCA_026706695.1_ASM2670669v1_genomic.fna.gz --refList GCA_026706695.1_ASM2670669v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706695.1_ASM2670669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:41:45,996] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:46,001] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 17:41:46,001] [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_009837205.1	s__RKRQ01 sp009837205	94.2812	437	566	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	98.20	97.22	0.91	0.89	4	-
GCA_009840385.1	s__RKRQ01 sp009840385	85.7818	412	566	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	96.93	96.24	0.92	0.88	7	-
GCA_007571325.1	s__RKRQ01 sp007571325	79.317	236	566	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	98.96	98.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-27 17:41:46,003] [INFO] GTDB search result was written to GCA_026706695.1_ASM2670669v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:41:46,004] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:41:46,007] [INFO] DFAST_QC result json was written to GCA_026706695.1_ASM2670669v1_genomic.fna/dqc_result.json
[2023-06-27 17:41:46,007] [INFO] DFAST_QC completed!
[2023-06-27 17:41:46,007] [INFO] Total running time: 0h0m41s