[2023-06-28 21:36:37,217] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:37,219] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:37,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference
[2023-06-28 21:36:40,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:40,190] [INFO] Task started: Prodigal
[2023-06-28 21:36:40,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b3ee17f-de84-42a7-ae72-71f708208333/GCA_017964185.1_ASM1796418v1_genomic.fna.gz | prodigal -d GCA_017964185.1_ASM1796418v1_genomic.fna/cds.fna -a GCA_017964185.1_ASM1796418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:42,229] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:42,230] [INFO] Task started: HMMsearch
[2023-06-28 21:36:42,230] [INFO] Running command: hmmsearch --tblout GCA_017964185.1_ASM1796418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/reference_markers.hmm GCA_017964185.1_ASM1796418v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:42,466] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:42,468] [INFO] Found 6/6 markers.
[2023-06-28 21:36:42,486] [INFO] Query marker FASTA was written to GCA_017964185.1_ASM1796418v1_genomic.fna/markers.fasta
[2023-06-28 21:36:42,486] [INFO] Task started: Blastn
[2023-06-28 21:36:42,486] [INFO] Running command: blastn -query GCA_017964185.1_ASM1796418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/reference_markers.fasta -out GCA_017964185.1_ASM1796418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:44,178] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:44,183] [INFO] Selected 13 target genomes.
[2023-06-28 21:36:44,183] [INFO] Target genome list was writen to GCA_017964185.1_ASM1796418v1_genomic.fna/target_genomes.txt
[2023-06-28 21:36:44,193] [INFO] Task started: fastANI
[2023-06-28 21:36:44,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3ee17f-de84-42a7-ae72-71f708208333/GCA_017964185.1_ASM1796418v1_genomic.fna.gz --refList GCA_017964185.1_ASM1796418v1_genomic.fna/target_genomes.txt --output GCA_017964185.1_ASM1796418v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:36:50,574] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:50,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:36:50,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:36:50,583] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:36:50,584] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:36:50,584] [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 21:36:50,587] [INFO] DFAST Taxonomy check result was written to GCA_017964185.1_ASM1796418v1_genomic.fna/tc_result.tsv
[2023-06-28 21:36:50,587] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:36:50,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:36:50,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/checkm_data
[2023-06-28 21:36:50,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:36:50,612] [INFO] Task started: CheckM
[2023-06-28 21:36:50,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017964185.1_ASM1796418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017964185.1_ASM1796418v1_genomic.fna/checkm_input GCA_017964185.1_ASM1796418v1_genomic.fna/checkm_result
[2023-06-28 21:37:05,320] [INFO] Task succeeded: CheckM
[2023-06-28 21:37:05,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:37:05,342] [INFO] ===== Completeness check finished =====
[2023-06-28 21:37:05,342] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:37:05,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017964185.1_ASM1796418v1_genomic.fna/markers.fasta)
[2023-06-28 21:37:05,343] [INFO] Task started: Blastn
[2023-06-28 21:37:05,343] [INFO] Running command: blastn -query GCA_017964185.1_ASM1796418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc957facc-87e0-4928-a53f-b9079dc3a966/dqc_reference/reference_markers_gtdb.fasta -out GCA_017964185.1_ASM1796418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:37:06,150] [INFO] Task succeeded: Blastn
[2023-06-28 21:37:06,155] [INFO] Selected 20 target genomes.
[2023-06-28 21:37:06,155] [INFO] Target genome list was writen to GCA_017964185.1_ASM1796418v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:37:06,161] [INFO] Task started: fastANI
[2023-06-28 21:37:06,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3ee17f-de84-42a7-ae72-71f708208333/GCA_017964185.1_ASM1796418v1_genomic.fna.gz --refList GCA_017964185.1_ASM1796418v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017964185.1_ASM1796418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:37:13,146] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:13,151] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:37:13,151] [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_017960845.1	s__Protoclostridium sp017960845	98.2498	258	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__Protoclostridium	95.0	98.12	97.96	0.82	0.78	3	conclusive
--------------------------------------------------------------------------------
[2023-06-28 21:37:13,176] [INFO] GTDB search result was written to GCA_017964185.1_ASM1796418v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:37:13,177] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:37:13,180] [INFO] DFAST_QC result json was written to GCA_017964185.1_ASM1796418v1_genomic.fna/dqc_result.json
[2023-06-28 21:37:13,181] [INFO] DFAST_QC completed!
[2023-06-28 21:37:13,181] [INFO] Total running time: 0h0m36s