[2023-06-05 10:22:52,069] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:22:52,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:22:52,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference
[2023-06-05 10:22:54,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:22:54,382] [INFO] Task started: Prodigal
[2023-06-05 10:22:54,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgb291a634-bf3e-4e1f-acfb-c71c10bf4b4e/GCA_001783375.1_ASM178337v1_genomic.fna.gz | prodigal -d GCA_001783375.1_ASM178337v1_genomic.fna/cds.fna -a GCA_001783375.1_ASM178337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:22:58,335] [INFO] Task succeeded: Prodigal
[2023-06-05 10:22:58,336] [INFO] Task started: HMMsearch
[2023-06-05 10:22:58,336] [INFO] Running command: hmmsearch --tblout GCA_001783375.1_ASM178337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/reference_markers.hmm GCA_001783375.1_ASM178337v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:22:58,530] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:22:58,532] [INFO] Found 6/6 markers.
[2023-06-05 10:22:58,545] [INFO] Query marker FASTA was written to GCA_001783375.1_ASM178337v1_genomic.fna/markers.fasta
[2023-06-05 10:22:58,545] [INFO] Task started: Blastn
[2023-06-05 10:22:58,545] [INFO] Running command: blastn -query GCA_001783375.1_ASM178337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/reference_markers.fasta -out GCA_001783375.1_ASM178337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:22:59,126] [INFO] Task succeeded: Blastn
[2023-06-05 10:22:59,130] [INFO] Selected 22 target genomes.
[2023-06-05 10:22:59,131] [INFO] Target genome list was writen to GCA_001783375.1_ASM178337v1_genomic.fna/target_genomes.txt
[2023-06-05 10:22:59,144] [INFO] Task started: fastANI
[2023-06-05 10:22:59,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgb291a634-bf3e-4e1f-acfb-c71c10bf4b4e/GCA_001783375.1_ASM178337v1_genomic.fna.gz --refList GCA_001783375.1_ASM178337v1_genomic.fna/target_genomes.txt --output GCA_001783375.1_ASM178337v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:23:16,465] [INFO] Task succeeded: fastANI
[2023-06-05 10:23:16,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:23:16,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:23:16,468] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:23:16,469] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:23:16,469] [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
--------------------------------------------------------------------------------
[2023-06-05 10:23:16,471] [INFO] DFAST Taxonomy check result was written to GCA_001783375.1_ASM178337v1_genomic.fna/tc_result.tsv
[2023-06-05 10:23:16,472] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:23:16,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:23:16,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/checkm_data
[2023-06-05 10:23:16,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:23:16,490] [INFO] Task started: CheckM
[2023-06-05 10:23:16,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001783375.1_ASM178337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001783375.1_ASM178337v1_genomic.fna/checkm_input GCA_001783375.1_ASM178337v1_genomic.fna/checkm_result
[2023-06-05 10:23:35,110] [INFO] Task succeeded: CheckM
[2023-06-05 10:23:35,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 10:23:35,132] [INFO] ===== Completeness check finished =====
[2023-06-05 10:23:35,132] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:23:35,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001783375.1_ASM178337v1_genomic.fna/markers.fasta)
[2023-06-05 10:23:35,133] [INFO] Task started: Blastn
[2023-06-05 10:23:35,133] [INFO] Running command: blastn -query GCA_001783375.1_ASM178337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7945a8-bf0e-4110-a000-1cc61a526298/dqc_reference/reference_markers_gtdb.fasta -out GCA_001783375.1_ASM178337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:23:35,984] [INFO] Task succeeded: Blastn
[2023-06-05 10:23:35,989] [INFO] Selected 26 target genomes.
[2023-06-05 10:23:35,990] [INFO] Target genome list was writen to GCA_001783375.1_ASM178337v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:23:36,058] [INFO] Task started: fastANI
[2023-06-05 10:23:36,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgb291a634-bf3e-4e1f-acfb-c71c10bf4b4e/GCA_001783375.1_ASM178337v1_genomic.fna.gz --refList GCA_001783375.1_ASM178337v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001783375.1_ASM178337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:23:41,702] [INFO] Task succeeded: fastANI
[2023-06-05 10:23:41,708] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 10:23:41,708] [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_001783355.1	s__UBA10103 sp001783355	86.3094	90	212	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA2100;g__UBA10103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001781445.1	s__UBA10103 sp001781445	78.6367	71	212	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA2100;g__UBA10103	95.0	99.83	99.83	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:23:41,715] [INFO] GTDB search result was written to GCA_001783375.1_ASM178337v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:23:41,716] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:23:41,721] [INFO] DFAST_QC result json was written to GCA_001783375.1_ASM178337v1_genomic.fna/dqc_result.json
[2023-06-05 10:23:41,721] [INFO] DFAST_QC completed!
[2023-06-05 10:23:41,721] [INFO] Total running time: 0h0m50s