[2023-06-19 04:59:07,454] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:07,456] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:07,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference
[2023-06-19 04:59:08,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:08,821] [INFO] Task started: Prodigal
[2023-06-19 04:59:08,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c8e466b-59db-4b6d-97fd-8dc8dd5b8d3d/GCA_018676855.1_ASM1867685v1_genomic.fna.gz | prodigal -d GCA_018676855.1_ASM1867685v1_genomic.fna/cds.fna -a GCA_018676855.1_ASM1867685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:10,923] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:10,924] [INFO] Task started: HMMsearch
[2023-06-19 04:59:10,924] [INFO] Running command: hmmsearch --tblout GCA_018676855.1_ASM1867685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/reference_markers.hmm GCA_018676855.1_ASM1867685v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:11,130] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:11,132] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8c8e466b-59db-4b6d-97fd-8dc8dd5b8d3d/GCA_018676855.1_ASM1867685v1_genomic.fna.gz]
[2023-06-19 04:59:11,153] [INFO] Query marker FASTA was written to GCA_018676855.1_ASM1867685v1_genomic.fna/markers.fasta
[2023-06-19 04:59:11,153] [INFO] Task started: Blastn
[2023-06-19 04:59:11,153] [INFO] Running command: blastn -query GCA_018676855.1_ASM1867685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/reference_markers.fasta -out GCA_018676855.1_ASM1867685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:12,853] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:12,858] [INFO] Selected 6 target genomes.
[2023-06-19 04:59:12,859] [INFO] Target genome list was writen to GCA_018676855.1_ASM1867685v1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:12,861] [INFO] Task started: fastANI
[2023-06-19 04:59:12,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8e466b-59db-4b6d-97fd-8dc8dd5b8d3d/GCA_018676855.1_ASM1867685v1_genomic.fna.gz --refList GCA_018676855.1_ASM1867685v1_genomic.fna/target_genomes.txt --output GCA_018676855.1_ASM1867685v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:59:15,452] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:15,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:59:15,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:59:15,455] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:59:15,455] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:59:15,455] [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 04:59:15,457] [INFO] DFAST Taxonomy check result was written to GCA_018676855.1_ASM1867685v1_genomic.fna/tc_result.tsv
[2023-06-19 04:59:15,458] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:59:15,458] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:59:15,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/checkm_data
[2023-06-19 04:59:15,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:59:15,476] [INFO] Task started: CheckM
[2023-06-19 04:59:15,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018676855.1_ASM1867685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018676855.1_ASM1867685v1_genomic.fna/checkm_input GCA_018676855.1_ASM1867685v1_genomic.fna/checkm_result
[2023-06-19 04:59:30,552] [INFO] Task succeeded: CheckM
[2023-06-19 04:59:30,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:59:30,581] [INFO] ===== Completeness check finished =====
[2023-06-19 04:59:30,582] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:59:30,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018676855.1_ASM1867685v1_genomic.fna/markers.fasta)
[2023-06-19 04:59:30,583] [INFO] Task started: Blastn
[2023-06-19 04:59:30,583] [INFO] Running command: blastn -query GCA_018676855.1_ASM1867685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3231855e-7b77-44b5-8326-64f75d0fbbe7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018676855.1_ASM1867685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:31,207] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:31,212] [INFO] Selected 9 target genomes.
[2023-06-19 04:59:31,212] [INFO] Target genome list was writen to GCA_018676855.1_ASM1867685v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:59:31,214] [INFO] Task started: fastANI
[2023-06-19 04:59:31,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8e466b-59db-4b6d-97fd-8dc8dd5b8d3d/GCA_018676855.1_ASM1867685v1_genomic.fna.gz --refList GCA_018676855.1_ASM1867685v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018676855.1_ASM1867685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:59:32,969] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:32,976] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:59:32,976] [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_018676855.1	s__PCYB01 sp018676855	100.0	312	312	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR9;g__PCYB01	95.0	99.98	99.98	0.99	0.97	5	conclusive
GCA_002762845.1	s__PCYB01 sp002762845	79.9681	164	312	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR9;g__PCYB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:59:32,979] [INFO] GTDB search result was written to GCA_018676855.1_ASM1867685v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:59:32,979] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:59:32,982] [INFO] DFAST_QC result json was written to GCA_018676855.1_ASM1867685v1_genomic.fna/dqc_result.json
[2023-06-19 04:59:32,983] [INFO] DFAST_QC completed!
[2023-06-19 04:59:32,983] [INFO] Total running time: 0h0m26s