[2023-06-13 05:35:16,530] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:35:16,532] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:35:16,532] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference
[2023-06-13 05:35:17,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:35:17,781] [INFO] Task started: Prodigal
[2023-06-13 05:35:17,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg72751784-3e66-4aeb-986c-bf24ab53fedd/GCA_022792235.1_ASM2279223v1_genomic.fna.gz | prodigal -d GCA_022792235.1_ASM2279223v1_genomic.fna/cds.fna -a GCA_022792235.1_ASM2279223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:35:18,989] [INFO] Task succeeded: Prodigal
[2023-06-13 05:35:18,990] [INFO] Task started: HMMsearch
[2023-06-13 05:35:18,990] [INFO] Running command: hmmsearch --tblout GCA_022792235.1_ASM2279223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/reference_markers.hmm GCA_022792235.1_ASM2279223v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:35:19,279] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:35:19,281] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg72751784-3e66-4aeb-986c-bf24ab53fedd/GCA_022792235.1_ASM2279223v1_genomic.fna.gz]
[2023-06-13 05:35:19,296] [INFO] Query marker FASTA was written to GCA_022792235.1_ASM2279223v1_genomic.fna/markers.fasta
[2023-06-13 05:35:19,297] [INFO] Task started: Blastn
[2023-06-13 05:35:19,297] [INFO] Running command: blastn -query GCA_022792235.1_ASM2279223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/reference_markers.fasta -out GCA_022792235.1_ASM2279223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:20,024] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:20,029] [INFO] Selected 25 target genomes.
[2023-06-13 05:35:20,030] [INFO] Target genome list was writen to GCA_022792235.1_ASM2279223v1_genomic.fna/target_genomes.txt
[2023-06-13 05:35:20,038] [INFO] Task started: fastANI
[2023-06-13 05:35:20,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg72751784-3e66-4aeb-986c-bf24ab53fedd/GCA_022792235.1_ASM2279223v1_genomic.fna.gz --refList GCA_022792235.1_ASM2279223v1_genomic.fna/target_genomes.txt --output GCA_022792235.1_ASM2279223v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:35:30,617] [INFO] Task succeeded: fastANI
[2023-06-13 05:35:30,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:35:30,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:35:30,620] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:35:30,620] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:35:30,621] [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
--------------------------------------------------------------------------------
[2023-06-13 05:35:30,623] [INFO] DFAST Taxonomy check result was written to GCA_022792235.1_ASM2279223v1_genomic.fna/tc_result.tsv
[2023-06-13 05:35:30,624] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:35:30,625] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:35:30,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/checkm_data
[2023-06-13 05:35:30,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:35:30,645] [INFO] Task started: CheckM
[2023-06-13 05:35:30,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792235.1_ASM2279223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792235.1_ASM2279223v1_genomic.fna/checkm_input GCA_022792235.1_ASM2279223v1_genomic.fna/checkm_result
[2023-06-13 05:35:42,801] [INFO] Task succeeded: CheckM
[2023-06-13 05:35:42,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:35:42,821] [INFO] ===== Completeness check finished =====
[2023-06-13 05:35:42,821] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:35:42,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792235.1_ASM2279223v1_genomic.fna/markers.fasta)
[2023-06-13 05:35:42,822] [INFO] Task started: Blastn
[2023-06-13 05:35:42,822] [INFO] Running command: blastn -query GCA_022792235.1_ASM2279223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7ce5f6e-a2dc-4a96-bd39-8a0ecac25e32/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792235.1_ASM2279223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:43,593] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:43,598] [INFO] Selected 22 target genomes.
[2023-06-13 05:35:43,598] [INFO] Target genome list was writen to GCA_022792235.1_ASM2279223v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:35:43,609] [INFO] Task started: fastANI
[2023-06-13 05:35:43,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg72751784-3e66-4aeb-986c-bf24ab53fedd/GCA_022792235.1_ASM2279223v1_genomic.fna.gz --refList GCA_022792235.1_ASM2279223v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792235.1_ASM2279223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:35:48,103] [INFO] Task succeeded: fastANI
[2023-06-13 05:35:48,108] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:35:48,108] [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_910576985.1	s__MGBC102946 sp910576985	78.1849	70	173	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC102946	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:35:48,110] [INFO] GTDB search result was written to GCA_022792235.1_ASM2279223v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:35:48,111] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:35:48,114] [INFO] DFAST_QC result json was written to GCA_022792235.1_ASM2279223v1_genomic.fna/dqc_result.json
[2023-06-13 05:35:48,114] [INFO] DFAST_QC completed!
[2023-06-13 05:35:48,114] [INFO] Total running time: 0h0m32s