[2023-06-19 04:14:26,996] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:26,999] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:26,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference
[2023-06-19 04:14:28,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:28,584] [INFO] Task started: Prodigal
[2023-06-19 04:14:28,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg65bf5a3a-90ce-4f8b-9975-902fe17692ff/GCA_018898035.1_ASM1889803v1_genomic.fna.gz | prodigal -d GCA_018898035.1_ASM1889803v1_genomic.fna/cds.fna -a GCA_018898035.1_ASM1889803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:30,048] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:30,049] [INFO] Task started: HMMsearch
[2023-06-19 04:14:30,049] [INFO] Running command: hmmsearch --tblout GCA_018898035.1_ASM1889803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/reference_markers.hmm GCA_018898035.1_ASM1889803v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:30,304] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:30,305] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg65bf5a3a-90ce-4f8b-9975-902fe17692ff/GCA_018898035.1_ASM1889803v1_genomic.fna.gz]
[2023-06-19 04:14:30,345] [INFO] Query marker FASTA was written to GCA_018898035.1_ASM1889803v1_genomic.fna/markers.fasta
[2023-06-19 04:14:30,346] [INFO] Task started: Blastn
[2023-06-19 04:14:30,346] [INFO] Running command: blastn -query GCA_018898035.1_ASM1889803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/reference_markers.fasta -out GCA_018898035.1_ASM1889803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:30,906] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:30,911] [INFO] Selected 5 target genomes.
[2023-06-19 04:14:30,911] [INFO] Target genome list was writen to GCA_018898035.1_ASM1889803v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:30,912] [INFO] Task started: fastANI
[2023-06-19 04:14:30,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg65bf5a3a-90ce-4f8b-9975-902fe17692ff/GCA_018898035.1_ASM1889803v1_genomic.fna.gz --refList GCA_018898035.1_ASM1889803v1_genomic.fna/target_genomes.txt --output GCA_018898035.1_ASM1889803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:33,544] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:33,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:33,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:33,547] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:14:33,548] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:14:33,548] [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
--------------------------------------------------------------------------------
[2023-06-19 04:14:33,550] [INFO] DFAST Taxonomy check result was written to GCA_018898035.1_ASM1889803v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:33,551] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:33,551] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:33,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/checkm_data
[2023-06-19 04:14:33,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:33,566] [INFO] Task started: CheckM
[2023-06-19 04:14:33,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018898035.1_ASM1889803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018898035.1_ASM1889803v1_genomic.fna/checkm_input GCA_018898035.1_ASM1889803v1_genomic.fna/checkm_result
[2023-06-19 04:14:47,529] [INFO] Task succeeded: CheckM
[2023-06-19 04:14:47,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:14:47,562] [INFO] ===== Completeness check finished =====
[2023-06-19 04:14:47,562] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:14:47,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018898035.1_ASM1889803v1_genomic.fna/markers.fasta)
[2023-06-19 04:14:47,563] [INFO] Task started: Blastn
[2023-06-19 04:14:47,564] [INFO] Running command: blastn -query GCA_018898035.1_ASM1889803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b27e7f-eb3c-467e-9556-e9bf71b53e96/dqc_reference/reference_markers_gtdb.fasta -out GCA_018898035.1_ASM1889803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:48,254] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:48,260] [INFO] Selected 8 target genomes.
[2023-06-19 04:14:48,261] [INFO] Target genome list was writen to GCA_018898035.1_ASM1889803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:14:48,266] [INFO] Task started: fastANI
[2023-06-19 04:14:48,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg65bf5a3a-90ce-4f8b-9975-902fe17692ff/GCA_018898035.1_ASM1889803v1_genomic.fna.gz --refList GCA_018898035.1_ASM1889803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018898035.1_ASM1889803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:14:50,107] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:50,110] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:14:50,110] [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_018896675.1	s__JAHIMK01 sp018896675	99.7465	138	159	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR17;g__JAHIMK01	95.0	99.51	99.29	0.88	0.87	3	conclusive
--------------------------------------------------------------------------------
[2023-06-19 04:14:50,113] [INFO] GTDB search result was written to GCA_018898035.1_ASM1889803v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:14:50,113] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:14:50,116] [INFO] DFAST_QC result json was written to GCA_018898035.1_ASM1889803v1_genomic.fna/dqc_result.json
[2023-06-19 04:14:50,117] [INFO] DFAST_QC completed!
[2023-06-19 04:14:50,117] [INFO] Total running time: 0h0m23s