[2023-06-17 18:03:36,483] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:03:36,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:03:36,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference
[2023-06-17 18:03:38,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:03:38,497] [INFO] Task started: Prodigal
[2023-06-17 18:03:38,497] [INFO] Running command: gunzip -c /var/lib/cwl/stga70cc99a-4d0e-4542-ae85-792619d83b1f/GCA_009922565.1_ASM992256v1_genomic.fna.gz | prodigal -d GCA_009922565.1_ASM992256v1_genomic.fna/cds.fna -a GCA_009922565.1_ASM992256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:03:50,249] [INFO] Task succeeded: Prodigal
[2023-06-17 18:03:50,249] [INFO] Task started: HMMsearch
[2023-06-17 18:03:50,250] [INFO] Running command: hmmsearch --tblout GCA_009922565.1_ASM992256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/reference_markers.hmm GCA_009922565.1_ASM992256v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:03:50,536] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:03:50,538] [INFO] Found 6/6 markers.
[2023-06-17 18:03:50,575] [INFO] Query marker FASTA was written to GCA_009922565.1_ASM992256v1_genomic.fna/markers.fasta
[2023-06-17 18:03:50,575] [INFO] Task started: Blastn
[2023-06-17 18:03:50,575] [INFO] Running command: blastn -query GCA_009922565.1_ASM992256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/reference_markers.fasta -out GCA_009922565.1_ASM992256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:03:51,143] [INFO] Task succeeded: Blastn
[2023-06-17 18:03:51,150] [INFO] Selected 17 target genomes.
[2023-06-17 18:03:51,150] [INFO] Target genome list was writen to GCA_009922565.1_ASM992256v1_genomic.fna/target_genomes.txt
[2023-06-17 18:03:51,153] [INFO] Task started: fastANI
[2023-06-17 18:03:51,153] [INFO] Running command: fastANI --query /var/lib/cwl/stga70cc99a-4d0e-4542-ae85-792619d83b1f/GCA_009922565.1_ASM992256v1_genomic.fna.gz --refList GCA_009922565.1_ASM992256v1_genomic.fna/target_genomes.txt --output GCA_009922565.1_ASM992256v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:04:04,678] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:04,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:04:04,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:04:04,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:04:04,681] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 18:04:04,681] [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
--------------------------------------------------------------------------------
[2023-06-17 18:04:04,683] [INFO] DFAST Taxonomy check result was written to GCA_009922565.1_ASM992256v1_genomic.fna/tc_result.tsv
[2023-06-17 18:04:04,683] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:04:04,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:04:04,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/checkm_data
[2023-06-17 18:04:04,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:04:04,728] [INFO] Task started: CheckM
[2023-06-17 18:04:04,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009922565.1_ASM992256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009922565.1_ASM992256v1_genomic.fna/checkm_input GCA_009922565.1_ASM992256v1_genomic.fna/checkm_result
[2023-06-17 18:04:42,790] [INFO] Task succeeded: CheckM
[2023-06-17 18:04:42,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:04:42,816] [INFO] ===== Completeness check finished =====
[2023-06-17 18:04:42,817] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:04:42,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009922565.1_ASM992256v1_genomic.fna/markers.fasta)
[2023-06-17 18:04:42,817] [INFO] Task started: Blastn
[2023-06-17 18:04:42,818] [INFO] Running command: blastn -query GCA_009922565.1_ASM992256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b425667-9c5c-4850-a1cd-7a038eb446d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_009922565.1_ASM992256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:04:43,558] [INFO] Task succeeded: Blastn
[2023-06-17 18:04:43,563] [INFO] Selected 15 target genomes.
[2023-06-17 18:04:43,563] [INFO] Target genome list was writen to GCA_009922565.1_ASM992256v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:04:43,567] [INFO] Task started: fastANI
[2023-06-17 18:04:43,567] [INFO] Running command: fastANI --query /var/lib/cwl/stga70cc99a-4d0e-4542-ae85-792619d83b1f/GCA_009922565.1_ASM992256v1_genomic.fna.gz --refList GCA_009922565.1_ASM992256v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009922565.1_ASM992256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:04:54,991] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:54,995] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:04:54,995] [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_002347925.1	s__UBA12225 sp002347925	99.3653	935	1099	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	98.21	95.05	0.90	0.85	18	conclusive
GCA_009693165.1	s__UBA12225 sp009693165	84.4585	548	1099	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836285.1	s__CAILQO01 sp903836285	76.7076	162	1099	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__CAILQO01	95.0	98.79	98.57	0.84	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-17 18:04:54,998] [INFO] GTDB search result was written to GCA_009922565.1_ASM992256v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:04:54,999] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:04:55,001] [INFO] DFAST_QC result json was written to GCA_009922565.1_ASM992256v1_genomic.fna/dqc_result.json
[2023-06-17 18:04:55,002] [INFO] DFAST_QC completed!
[2023-06-17 18:04:55,002] [INFO] Total running time: 0h1m19s