[2023-06-18 22:24:48,686] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:24:48,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:24:48,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference
[2023-06-18 22:24:50,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:24:50,405] [INFO] Task started: Prodigal
[2023-06-18 22:24:50,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgf653719c-df36-4acf-8384-3841dd905279/GCA_013331775.1_ASM1333177v1_genomic.fna.gz | prodigal -d GCA_013331775.1_ASM1333177v1_genomic.fna/cds.fna -a GCA_013331775.1_ASM1333177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:24:52,118] [INFO] Task succeeded: Prodigal
[2023-06-18 22:24:52,118] [INFO] Task started: HMMsearch
[2023-06-18 22:24:52,118] [INFO] Running command: hmmsearch --tblout GCA_013331775.1_ASM1333177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/reference_markers.hmm GCA_013331775.1_ASM1333177v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:24:52,328] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:24:52,330] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf653719c-df36-4acf-8384-3841dd905279/GCA_013331775.1_ASM1333177v1_genomic.fna.gz]
[2023-06-18 22:24:52,347] [INFO] Query marker FASTA was written to GCA_013331775.1_ASM1333177v1_genomic.fna/markers.fasta
[2023-06-18 22:24:52,348] [INFO] Task started: Blastn
[2023-06-18 22:24:52,348] [INFO] Running command: blastn -query GCA_013331775.1_ASM1333177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/reference_markers.fasta -out GCA_013331775.1_ASM1333177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:24:52,907] [INFO] Task succeeded: Blastn
[2023-06-18 22:24:52,912] [INFO] Selected 5 target genomes.
[2023-06-18 22:24:52,913] [INFO] Target genome list was writen to GCA_013331775.1_ASM1333177v1_genomic.fna/target_genomes.txt
[2023-06-18 22:24:52,914] [INFO] Task started: fastANI
[2023-06-18 22:24:52,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgf653719c-df36-4acf-8384-3841dd905279/GCA_013331775.1_ASM1333177v1_genomic.fna.gz --refList GCA_013331775.1_ASM1333177v1_genomic.fna/target_genomes.txt --output GCA_013331775.1_ASM1333177v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:24:55,329] [INFO] Task succeeded: fastANI
[2023-06-18 22:24:55,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:24:55,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:24:55,331] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:24:55,331] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:24:55,331] [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
--------------------------------------------------------------------------------
[2023-06-18 22:24:55,336] [INFO] DFAST Taxonomy check result was written to GCA_013331775.1_ASM1333177v1_genomic.fna/tc_result.tsv
[2023-06-18 22:24:55,338] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:24:55,338] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:24:55,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/checkm_data
[2023-06-18 22:24:55,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:24:55,357] [INFO] Task started: CheckM
[2023-06-18 22:24:55,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013331775.1_ASM1333177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013331775.1_ASM1333177v1_genomic.fna/checkm_input GCA_013331775.1_ASM1333177v1_genomic.fna/checkm_result
[2023-06-18 22:25:09,571] [INFO] Task succeeded: CheckM
[2023-06-18 22:25:09,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 22:25:09,605] [INFO] ===== Completeness check finished =====
[2023-06-18 22:25:09,606] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:25:09,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013331775.1_ASM1333177v1_genomic.fna/markers.fasta)
[2023-06-18 22:25:09,607] [INFO] Task started: Blastn
[2023-06-18 22:25:09,607] [INFO] Running command: blastn -query GCA_013331775.1_ASM1333177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2e34be-4d06-4fee-9662-b929bf2a6c8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_013331775.1_ASM1333177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:25:10,252] [INFO] Task succeeded: Blastn
[2023-06-18 22:25:10,255] [INFO] Selected 6 target genomes.
[2023-06-18 22:25:10,255] [INFO] Target genome list was writen to GCA_013331775.1_ASM1333177v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:25:10,260] [INFO] Task started: fastANI
[2023-06-18 22:25:10,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgf653719c-df36-4acf-8384-3841dd905279/GCA_013331775.1_ASM1333177v1_genomic.fna.gz --refList GCA_013331775.1_ASM1333177v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013331775.1_ASM1333177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:25:11,496] [INFO] Task succeeded: fastANI
[2023-06-18 22:25:11,500] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:25:11,500] [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_000806155.1	s__GW2011-AR18 sp000806155	99.8334	252	312	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR18;g__GW2011-AR18	95.0	99.82	99.81	0.90	0.87	3	conclusive
--------------------------------------------------------------------------------
[2023-06-18 22:25:11,503] [INFO] GTDB search result was written to GCA_013331775.1_ASM1333177v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:25:11,503] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:25:11,505] [INFO] DFAST_QC result json was written to GCA_013331775.1_ASM1333177v1_genomic.fna/dqc_result.json
[2023-06-18 22:25:11,506] [INFO] DFAST_QC completed!
[2023-06-18 22:25:11,506] [INFO] Total running time: 0h0m23s