[2023-06-08 05:14:04,686] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:14:04,688] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:14:04,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference
[2023-06-08 05:14:05,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:14:05,865] [INFO] Task started: Prodigal
[2023-06-08 05:14:05,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eb50d3c-0d2b-45a3-8713-9add1af63a0c/GCA_902635955.1_AG-916-A23_genomic.fna.gz | prodigal -d GCA_902635955.1_AG-916-A23_genomic.fna/cds.fna -a GCA_902635955.1_AG-916-A23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:14:07,242] [INFO] Task succeeded: Prodigal
[2023-06-08 05:14:07,242] [INFO] Task started: HMMsearch
[2023-06-08 05:14:07,242] [INFO] Running command: hmmsearch --tblout GCA_902635955.1_AG-916-A23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/reference_markers.hmm GCA_902635955.1_AG-916-A23_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:14:07,389] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:14:07,390] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8eb50d3c-0d2b-45a3-8713-9add1af63a0c/GCA_902635955.1_AG-916-A23_genomic.fna.gz]
[2023-06-08 05:14:07,402] [INFO] Query marker FASTA was written to GCA_902635955.1_AG-916-A23_genomic.fna/markers.fasta
[2023-06-08 05:14:07,402] [INFO] Task started: Blastn
[2023-06-08 05:14:07,403] [INFO] Running command: blastn -query GCA_902635955.1_AG-916-A23_genomic.fna/markers.fasta -db /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/reference_markers.fasta -out GCA_902635955.1_AG-916-A23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:07,867] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:07,870] [INFO] Selected 5 target genomes.
[2023-06-08 05:14:07,870] [INFO] Target genome list was writen to GCA_902635955.1_AG-916-A23_genomic.fna/target_genomes.txt
[2023-06-08 05:14:07,871] [INFO] Task started: fastANI
[2023-06-08 05:14:07,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb50d3c-0d2b-45a3-8713-9add1af63a0c/GCA_902635955.1_AG-916-A23_genomic.fna.gz --refList GCA_902635955.1_AG-916-A23_genomic.fna/target_genomes.txt --output GCA_902635955.1_AG-916-A23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:14:09,405] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:09,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:14:09,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:14:09,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:14:09,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:14:09,407] [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
--------------------------------------------------------------------------------
[2023-06-08 05:14:09,408] [INFO] DFAST Taxonomy check result was written to GCA_902635955.1_AG-916-A23_genomic.fna/tc_result.tsv
[2023-06-08 05:14:09,409] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:14:09,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:14:09,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/checkm_data
[2023-06-08 05:14:09,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:14:09,422] [INFO] Task started: CheckM
[2023-06-08 05:14:09,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635955.1_AG-916-A23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635955.1_AG-916-A23_genomic.fna/checkm_input GCA_902635955.1_AG-916-A23_genomic.fna/checkm_result
[2023-06-08 05:14:20,990] [INFO] Task succeeded: CheckM
[2023-06-08 05:14:20,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:14:21,004] [INFO] ===== Completeness check finished =====
[2023-06-08 05:14:21,004] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:14:21,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635955.1_AG-916-A23_genomic.fna/markers.fasta)
[2023-06-08 05:14:21,005] [INFO] Task started: Blastn
[2023-06-08 05:14:21,005] [INFO] Running command: blastn -query GCA_902635955.1_AG-916-A23_genomic.fna/markers.fasta -db /var/lib/cwl/stg33222a35-a8ac-40be-9f31-493b3914a866/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635955.1_AG-916-A23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:21,434] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:21,437] [INFO] Selected 9 target genomes.
[2023-06-08 05:14:21,438] [INFO] Target genome list was writen to GCA_902635955.1_AG-916-A23_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:14:21,439] [INFO] Task started: fastANI
[2023-06-08 05:14:21,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb50d3c-0d2b-45a3-8713-9add1af63a0c/GCA_902635955.1_AG-916-A23_genomic.fna.gz --refList GCA_902635955.1_AG-916-A23_genomic.fna/target_genomes_gtdb.txt --output GCA_902635955.1_AG-916-A23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:14:23,290] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:23,297] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:14:23,297] [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_902616715.1	s__AG-339-G14 sp902616715	98.9399	247	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	conclusive
GCA_902527995.1	s__AG-339-G14 sp902527995	89.8514	161	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213955.1	s__AG-339-G14 sp004213955	85.991	201	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536295.1	s__AG-339-G14 sp902536295	80.7139	141	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.79	97.73	0.85	0.77	3	-
GCA_902562135.1	s__AG-339-G14 sp902562135	80.4583	125	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.66	97.66	0.82	0.82	2	-
GCA_902613455.1	s__AG-339-G14 sp902613455	79.6286	132	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	-
--------------------------------------------------------------------------------
[2023-06-08 05:14:23,299] [INFO] GTDB search result was written to GCA_902635955.1_AG-916-A23_genomic.fna/result_gtdb.tsv
[2023-06-08 05:14:23,299] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:14:23,301] [INFO] DFAST_QC result json was written to GCA_902635955.1_AG-916-A23_genomic.fna/dqc_result.json
[2023-06-08 05:14:23,302] [INFO] DFAST_QC completed!
[2023-06-08 05:14:23,302] [INFO] Total running time: 0h0m19s