[2023-06-30 14:53:54,249] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:53:54,252] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:53:54,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference
[2023-06-30 14:53:55,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:53:55,816] [INFO] Task started: Prodigal
[2023-06-30 14:53:55,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg584954c7-94ec-45b7-938d-304ddd5e9f2d/GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna.gz | prodigal -d GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/cds.fna -a GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:02,764] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:02,765] [INFO] Task started: HMMsearch
[2023-06-30 14:54:02,765] [INFO] Running command: hmmsearch --tblout GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/reference_markers.hmm GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:03,059] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:03,061] [INFO] Found 6/6 markers.
[2023-06-30 14:54:03,095] [INFO] Query marker FASTA was written to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/markers.fasta
[2023-06-30 14:54:03,095] [INFO] Task started: Blastn
[2023-06-30 14:54:03,095] [INFO] Running command: blastn -query GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/markers.fasta -db /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/reference_markers.fasta -out GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:03,694] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:03,700] [INFO] Selected 29 target genomes.
[2023-06-30 14:54:03,701] [INFO] Target genome list was writen to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/target_genomes.txt
[2023-06-30 14:54:03,709] [INFO] Task started: fastANI
[2023-06-30 14:54:03,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg584954c7-94ec-45b7-938d-304ddd5e9f2d/GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna.gz --refList GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/target_genomes.txt --output GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:24,777] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:24,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:24,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:24,781] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:24,781] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:54:24,781] [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
--------------------------------------------------------------------------------
[2023-06-30 14:54:24,784] [INFO] DFAST Taxonomy check result was written to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/tc_result.tsv
[2023-06-30 14:54:24,785] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:24,785] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:24,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/checkm_data
[2023-06-30 14:54:24,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:24,827] [INFO] Task started: CheckM
[2023-06-30 14:54:24,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/checkm_input GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/checkm_result
[2023-06-30 14:54:52,571] [INFO] Task succeeded: CheckM
[2023-06-30 14:54:52,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:54:52,611] [INFO] ===== Completeness check finished =====
[2023-06-30 14:54:52,612] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:54:52,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/markers.fasta)
[2023-06-30 14:54:52,613] [INFO] Task started: Blastn
[2023-06-30 14:54:52,613] [INFO] Running command: blastn -query GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/markers.fasta -db /var/lib/cwl/stg22f6a037-9d8d-4622-93fe-eb45faa6fc18/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:53,445] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:53,450] [INFO] Selected 31 target genomes.
[2023-06-30 14:54:53,450] [INFO] Target genome list was writen to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:54:53,468] [INFO] Task started: fastANI
[2023-06-30 14:54:53,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg584954c7-94ec-45b7-938d-304ddd5e9f2d/GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna.gz --refList GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/target_genomes_gtdb.txt --output GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:10,080] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:10,084] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:55:10,084] [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_903862805.1	s__CAIOZP01 sp903862805	100.0	615	622	d__Bacteria;p__Fibrobacterota;c__Chitinivibrionia;o__Chitinivibrionales;f__CAIOZP01;g__CAIOZP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-30 14:55:10,087] [INFO] GTDB search result was written to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:10,087] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:10,090] [INFO] DFAST_QC result json was written to GCA_903862805.1_freshwater_MAG_---_VK_bin-2524_genomic.fna/dqc_result.json
[2023-06-30 14:55:10,090] [INFO] DFAST_QC completed!
[2023-06-30 14:55:10,090] [INFO] Total running time: 0h1m16s