[2023-06-19 05:51:39,824] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:39,834] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:39,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference
[2023-06-19 05:51:41,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:41,103] [INFO] Task started: Prodigal
[2023-06-19 05:51:41,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgba96fc98-c80a-4216-82de-4b0187cac741/GCA_018672335.1_ASM1867233v1_genomic.fna.gz | prodigal -d GCA_018672335.1_ASM1867233v1_genomic.fna/cds.fna -a GCA_018672335.1_ASM1867233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:43,322] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:43,323] [INFO] Task started: HMMsearch
[2023-06-19 05:51:43,323] [INFO] Running command: hmmsearch --tblout GCA_018672335.1_ASM1867233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/reference_markers.hmm GCA_018672335.1_ASM1867233v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:43,550] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:43,553] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgba96fc98-c80a-4216-82de-4b0187cac741/GCA_018672335.1_ASM1867233v1_genomic.fna.gz]
[2023-06-19 05:51:43,577] [INFO] Query marker FASTA was written to GCA_018672335.1_ASM1867233v1_genomic.fna/markers.fasta
[2023-06-19 05:51:43,577] [INFO] Task started: Blastn
[2023-06-19 05:51:43,577] [INFO] Running command: blastn -query GCA_018672335.1_ASM1867233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/reference_markers.fasta -out GCA_018672335.1_ASM1867233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:46,658] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:46,661] [INFO] Selected 5 target genomes.
[2023-06-19 05:51:46,662] [INFO] Target genome list was writen to GCA_018672335.1_ASM1867233v1_genomic.fna/target_genomes.txt
[2023-06-19 05:51:46,663] [INFO] Task started: fastANI
[2023-06-19 05:51:46,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgba96fc98-c80a-4216-82de-4b0187cac741/GCA_018672335.1_ASM1867233v1_genomic.fna.gz --refList GCA_018672335.1_ASM1867233v1_genomic.fna/target_genomes.txt --output GCA_018672335.1_ASM1867233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:51:49,317] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:49,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:51:49,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:51:49,320] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:51:49,320] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:51:49,320] [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 05:51:49,322] [INFO] DFAST Taxonomy check result was written to GCA_018672335.1_ASM1867233v1_genomic.fna/tc_result.tsv
[2023-06-19 05:51:49,322] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:51:49,322] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:51:49,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/checkm_data
[2023-06-19 05:51:49,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:51:49,344] [INFO] Task started: CheckM
[2023-06-19 05:51:49,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018672335.1_ASM1867233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018672335.1_ASM1867233v1_genomic.fna/checkm_input GCA_018672335.1_ASM1867233v1_genomic.fna/checkm_result
[2023-06-19 05:52:06,196] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:06,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:52:06,223] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:06,224] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:06,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018672335.1_ASM1867233v1_genomic.fna/markers.fasta)
[2023-06-19 05:52:06,225] [INFO] Task started: Blastn
[2023-06-19 05:52:06,225] [INFO] Running command: blastn -query GCA_018672335.1_ASM1867233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e542d13-386c-4a13-9fba-f28caf1a9221/dqc_reference/reference_markers_gtdb.fasta -out GCA_018672335.1_ASM1867233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:06,699] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:06,705] [INFO] Selected 7 target genomes.
[2023-06-19 05:52:06,706] [INFO] Target genome list was writen to GCA_018672335.1_ASM1867233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:06,707] [INFO] Task started: fastANI
[2023-06-19 05:52:06,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgba96fc98-c80a-4216-82de-4b0187cac741/GCA_018672335.1_ASM1867233v1_genomic.fna.gz --refList GCA_018672335.1_ASM1867233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018672335.1_ASM1867233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:52:09,445] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:09,448] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:52:09,448] [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_018653365.1	s__JABIAG01 sp018653365	99.9992	358	366	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__JABIAG01;g__JABIAG01	95.0	100.00	99.99	0.99	0.99	7	conclusive
--------------------------------------------------------------------------------
[2023-06-19 05:52:09,450] [INFO] GTDB search result was written to GCA_018672335.1_ASM1867233v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:52:09,451] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:52:09,453] [INFO] DFAST_QC result json was written to GCA_018672335.1_ASM1867233v1_genomic.fna/dqc_result.json
[2023-06-19 05:52:09,453] [INFO] DFAST_QC completed!
[2023-06-19 05:52:09,453] [INFO] Total running time: 0h0m30s