[2023-06-29 03:46:31,821] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:46:31,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:46:31,930] [INFO] DQC Reference Directory: /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference
[2023-06-29 03:46:33,878] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:46:33,879] [INFO] Task started: Prodigal
[2023-06-29 03:46:33,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg319a744f-59e1-4f6c-9d67-77c5af4e7872/GCA_015491245.1_ASM1549124v1_genomic.fna.gz | prodigal -d GCA_015491245.1_ASM1549124v1_genomic.fna/cds.fna -a GCA_015491245.1_ASM1549124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:46:39,956] [INFO] Task succeeded: Prodigal
[2023-06-29 03:46:39,957] [INFO] Task started: HMMsearch
[2023-06-29 03:46:39,957] [INFO] Running command: hmmsearch --tblout GCA_015491245.1_ASM1549124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/reference_markers.hmm GCA_015491245.1_ASM1549124v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:46:40,160] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:46:40,162] [INFO] Found 6/6 markers.
[2023-06-29 03:46:40,179] [INFO] Query marker FASTA was written to GCA_015491245.1_ASM1549124v1_genomic.fna/markers.fasta
[2023-06-29 03:46:40,179] [INFO] Task started: Blastn
[2023-06-29 03:46:40,180] [INFO] Running command: blastn -query GCA_015491245.1_ASM1549124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/reference_markers.fasta -out GCA_015491245.1_ASM1549124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:46:40,772] [INFO] Task succeeded: Blastn
[2023-06-29 03:46:40,776] [INFO] Selected 15 target genomes.
[2023-06-29 03:46:40,777] [INFO] Target genome list was writen to GCA_015491245.1_ASM1549124v1_genomic.fna/target_genomes.txt
[2023-06-29 03:46:40,781] [INFO] Task started: fastANI
[2023-06-29 03:46:40,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg319a744f-59e1-4f6c-9d67-77c5af4e7872/GCA_015491245.1_ASM1549124v1_genomic.fna.gz --refList GCA_015491245.1_ASM1549124v1_genomic.fna/target_genomes.txt --output GCA_015491245.1_ASM1549124v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:46:49,047] [INFO] Task succeeded: fastANI
[2023-06-29 03:46:49,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:46:49,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:46:49,049] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:46:49,049] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 03:46:49,050] [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
--------------------------------------------------------------------------------
[2023-06-29 03:46:49,052] [INFO] DFAST Taxonomy check result was written to GCA_015491245.1_ASM1549124v1_genomic.fna/tc_result.tsv
[2023-06-29 03:46:49,053] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:46:49,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:46:49,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/checkm_data
[2023-06-29 03:46:49,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:46:49,072] [INFO] Task started: CheckM
[2023-06-29 03:46:49,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015491245.1_ASM1549124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015491245.1_ASM1549124v1_genomic.fna/checkm_input GCA_015491245.1_ASM1549124v1_genomic.fna/checkm_result
[2023-06-29 03:47:12,208] [INFO] Task succeeded: CheckM
[2023-06-29 03:47:12,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:47:12,230] [INFO] ===== Completeness check finished =====
[2023-06-29 03:47:12,231] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:47:12,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015491245.1_ASM1549124v1_genomic.fna/markers.fasta)
[2023-06-29 03:47:12,231] [INFO] Task started: Blastn
[2023-06-29 03:47:12,232] [INFO] Running command: blastn -query GCA_015491245.1_ASM1549124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge23338d7-91bc-42e3-9772-cf67ca4104a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_015491245.1_ASM1549124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:13,070] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:13,076] [INFO] Selected 17 target genomes.
[2023-06-29 03:47:13,076] [INFO] Target genome list was writen to GCA_015491245.1_ASM1549124v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:47:13,086] [INFO] Task started: fastANI
[2023-06-29 03:47:13,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg319a744f-59e1-4f6c-9d67-77c5af4e7872/GCA_015491245.1_ASM1549124v1_genomic.fna.gz --refList GCA_015491245.1_ASM1549124v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015491245.1_ASM1549124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:47:18,254] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:18,258] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:47:18,259] [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_015491245.1	s__WFWH01 sp015491245	100.0	261	264	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__J119;g__WFWH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-29 03:47:18,261] [INFO] GTDB search result was written to GCA_015491245.1_ASM1549124v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:47:18,262] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:47:18,264] [INFO] DFAST_QC result json was written to GCA_015491245.1_ASM1549124v1_genomic.fna/dqc_result.json
[2023-06-29 03:47:18,265] [INFO] DFAST_QC completed!
[2023-06-29 03:47:18,265] [INFO] Total running time: 0h0m46s