[2023-06-28 14:06:17,314] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:06:17,316] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:06:17,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference
[2023-06-28 14:06:18,617] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:06:18,618] [INFO] Task started: Prodigal
[2023-06-28 14:06:18,618] [INFO] Running command: gunzip -c /var/lib/cwl/stgb70cdc02-33af-4901-b78e-538707645589/GCA_012962115.1_ASM1296211v1_genomic.fna.gz | prodigal -d GCA_012962115.1_ASM1296211v1_genomic.fna/cds.fna -a GCA_012962115.1_ASM1296211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:21,608] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:21,609] [INFO] Task started: HMMsearch
[2023-06-28 14:06:21,609] [INFO] Running command: hmmsearch --tblout GCA_012962115.1_ASM1296211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/reference_markers.hmm GCA_012962115.1_ASM1296211v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:21,799] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:21,800] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb70cdc02-33af-4901-b78e-538707645589/GCA_012962115.1_ASM1296211v1_genomic.fna.gz]
[2023-06-28 14:06:21,818] [INFO] Query marker FASTA was written to GCA_012962115.1_ASM1296211v1_genomic.fna/markers.fasta
[2023-06-28 14:06:21,818] [INFO] Task started: Blastn
[2023-06-28 14:06:21,818] [INFO] Running command: blastn -query GCA_012962115.1_ASM1296211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/reference_markers.fasta -out GCA_012962115.1_ASM1296211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:22,381] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:22,384] [INFO] Selected 10 target genomes.
[2023-06-28 14:06:22,385] [INFO] Target genome list was writen to GCA_012962115.1_ASM1296211v1_genomic.fna/target_genomes.txt
[2023-06-28 14:06:22,390] [INFO] Task started: fastANI
[2023-06-28 14:06:22,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgb70cdc02-33af-4901-b78e-538707645589/GCA_012962115.1_ASM1296211v1_genomic.fna.gz --refList GCA_012962115.1_ASM1296211v1_genomic.fna/target_genomes.txt --output GCA_012962115.1_ASM1296211v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:26,503] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:26,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:26,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:26,505] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:26,505] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:06:26,505] [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 14:06:26,507] [INFO] DFAST Taxonomy check result was written to GCA_012962115.1_ASM1296211v1_genomic.fna/tc_result.tsv
[2023-06-28 14:06:26,508] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:26,508] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:26,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/checkm_data
[2023-06-28 14:06:26,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:26,529] [INFO] Task started: CheckM
[2023-06-28 14:06:26,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012962115.1_ASM1296211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012962115.1_ASM1296211v1_genomic.fna/checkm_input GCA_012962115.1_ASM1296211v1_genomic.fna/checkm_result
[2023-06-28 14:06:43,395] [INFO] Task succeeded: CheckM
[2023-06-28 14:06:43,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.56%
Contamintation: 8.80%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:06:43,422] [INFO] ===== Completeness check finished =====
[2023-06-28 14:06:43,422] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:06:43,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012962115.1_ASM1296211v1_genomic.fna/markers.fasta)
[2023-06-28 14:06:43,423] [INFO] Task started: Blastn
[2023-06-28 14:06:43,423] [INFO] Running command: blastn -query GCA_012962115.1_ASM1296211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg740baa5b-cf82-46ac-9bdc-b608f04daaf9/dqc_reference/reference_markers_gtdb.fasta -out GCA_012962115.1_ASM1296211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:44,148] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:44,152] [INFO] Selected 11 target genomes.
[2023-06-28 14:06:44,152] [INFO] Target genome list was writen to GCA_012962115.1_ASM1296211v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:06:44,163] [INFO] Task started: fastANI
[2023-06-28 14:06:44,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgb70cdc02-33af-4901-b78e-538707645589/GCA_012962115.1_ASM1296211v1_genomic.fna.gz --refList GCA_012962115.1_ASM1296211v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012962115.1_ASM1296211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:06:47,134] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:47,137] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:06:47,137] [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_016839105.1	s__SZUA-1403 sp016839105	99.0395	119	135	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__CAIRYL01;f__CAIRYL01;g__SZUA-1403	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-28 14:06:47,139] [INFO] GTDB search result was written to GCA_012962115.1_ASM1296211v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:06:47,140] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:06:47,143] [INFO] DFAST_QC result json was written to GCA_012962115.1_ASM1296211v1_genomic.fna/dqc_result.json
[2023-06-28 14:06:47,143] [INFO] DFAST_QC completed!
[2023-06-28 14:06:47,143] [INFO] Total running time: 0h0m30s