[2023-06-19 12:40:30,687] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:40:30,690] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:40:30,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference
[2023-06-19 12:40:33,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:40:33,014] [INFO] Task started: Prodigal
[2023-06-19 12:40:33,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg65fce47a-bbc2-4672-90b5-e723725aa5b2/GCA_018303645.1_ASM1830364v1_genomic.fna.gz | prodigal -d GCA_018303645.1_ASM1830364v1_genomic.fna/cds.fna -a GCA_018303645.1_ASM1830364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:40:35,382] [INFO] Task succeeded: Prodigal
[2023-06-19 12:40:35,382] [INFO] Task started: HMMsearch
[2023-06-19 12:40:35,382] [INFO] Running command: hmmsearch --tblout GCA_018303645.1_ASM1830364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/reference_markers.hmm GCA_018303645.1_ASM1830364v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:40:35,568] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:40:35,570] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg65fce47a-bbc2-4672-90b5-e723725aa5b2/GCA_018303645.1_ASM1830364v1_genomic.fna.gz]
[2023-06-19 12:40:35,590] [INFO] Query marker FASTA was written to GCA_018303645.1_ASM1830364v1_genomic.fna/markers.fasta
[2023-06-19 12:40:35,591] [INFO] Task started: Blastn
[2023-06-19 12:40:35,591] [INFO] Running command: blastn -query GCA_018303645.1_ASM1830364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/reference_markers.fasta -out GCA_018303645.1_ASM1830364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:40:37,771] [INFO] Task succeeded: Blastn
[2023-06-19 12:40:37,776] [INFO] Selected 5 target genomes.
[2023-06-19 12:40:37,777] [INFO] Target genome list was writen to GCA_018303645.1_ASM1830364v1_genomic.fna/target_genomes.txt
[2023-06-19 12:40:37,794] [INFO] Task started: fastANI
[2023-06-19 12:40:37,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fce47a-bbc2-4672-90b5-e723725aa5b2/GCA_018303645.1_ASM1830364v1_genomic.fna.gz --refList GCA_018303645.1_ASM1830364v1_genomic.fna/target_genomes.txt --output GCA_018303645.1_ASM1830364v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:40:41,110] [INFO] Task succeeded: fastANI
[2023-06-19 12:40:41,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:40:41,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:40:41,113] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:40:41,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:40:41,113] [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 12:40:41,115] [INFO] DFAST Taxonomy check result was written to GCA_018303645.1_ASM1830364v1_genomic.fna/tc_result.tsv
[2023-06-19 12:40:41,116] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:40:41,116] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:40:41,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/checkm_data
[2023-06-19 12:40:41,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:40:41,137] [INFO] Task started: CheckM
[2023-06-19 12:40:41,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018303645.1_ASM1830364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018303645.1_ASM1830364v1_genomic.fna/checkm_input GCA_018303645.1_ASM1830364v1_genomic.fna/checkm_result
[2023-06-19 12:40:58,664] [INFO] Task succeeded: CheckM
[2023-06-19 12:40:58,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:40:58,684] [INFO] ===== Completeness check finished =====
[2023-06-19 12:40:58,684] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:40:58,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018303645.1_ASM1830364v1_genomic.fna/markers.fasta)
[2023-06-19 12:40:58,685] [INFO] Task started: Blastn
[2023-06-19 12:40:58,685] [INFO] Running command: blastn -query GCA_018303645.1_ASM1830364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2568518-fa86-4cfc-b49f-eb64dd18e5aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_018303645.1_ASM1830364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:40:59,321] [INFO] Task succeeded: Blastn
[2023-06-19 12:40:59,326] [INFO] Selected 8 target genomes.
[2023-06-19 12:40:59,326] [INFO] Target genome list was writen to GCA_018303645.1_ASM1830364v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:40:59,333] [INFO] Task started: fastANI
[2023-06-19 12:40:59,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fce47a-bbc2-4672-90b5-e723725aa5b2/GCA_018303645.1_ASM1830364v1_genomic.fna.gz --refList GCA_018303645.1_ASM1830364v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018303645.1_ASM1830364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:41:01,126] [INFO] Task succeeded: fastANI
[2023-06-19 12:41:01,139] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:41:01,139] [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_018303645.1	s__GCA-2688775 sp018303645	100.0	327	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018303685.1	s__GCA-2688775 sp018303685	81.5327	147	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016181305.1	s__GCA-2688775 sp016181305	80.9159	139	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018303505.1	s__GCA-2688775 sp018303505	77.9075	94	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018303655.1	s__GCA-2688775 sp018303655	77.7201	114	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185755.1	s__GCA-2688775 sp016185755	77.0553	72	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016188245.1	s__GCA-2688775 sp016188245	77.0277	87	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185805.1	s__GCA-2688775 sp016185805	76.6076	60	335	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GCA-2688775	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:41:01,144] [INFO] GTDB search result was written to GCA_018303645.1_ASM1830364v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:41:01,145] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:41:01,148] [INFO] DFAST_QC result json was written to GCA_018303645.1_ASM1830364v1_genomic.fna/dqc_result.json
[2023-06-19 12:41:01,149] [INFO] DFAST_QC completed!
[2023-06-19 12:41:01,149] [INFO] Total running time: 0h0m30s