[2023-03-18 06:02:58,279] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:02:58,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:02:58,279] [INFO] DQC Reference Directory: /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference
[2023-03-18 06:03:00,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:03:00,171] [INFO] Task started: Prodigal
[2023-03-18 06:03:00,171] [INFO] Running command: cat /var/lib/cwl/stgff567b69-f617-4c94-ab98-49efd616e2e5/OceanDNA-b2756.fa | prodigal -d OceanDNA-b2756/cds.fna -a OceanDNA-b2756/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:03:07,852] [INFO] Task succeeded: Prodigal
[2023-03-18 06:03:07,853] [INFO] Task started: HMMsearch
[2023-03-18 06:03:07,853] [INFO] Running command: hmmsearch --tblout OceanDNA-b2756/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/reference_markers.hmm OceanDNA-b2756/protein.faa > /dev/null
[2023-03-18 06:03:08,031] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:03:08,032] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgff567b69-f617-4c94-ab98-49efd616e2e5/OceanDNA-b2756.fa]
[2023-03-18 06:03:08,041] [INFO] Query marker FASTA was written to OceanDNA-b2756/markers.fasta
[2023-03-18 06:03:08,042] [INFO] Task started: Blastn
[2023-03-18 06:03:08,042] [INFO] Running command: blastn -query OceanDNA-b2756/markers.fasta -db /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/reference_markers.fasta -out OceanDNA-b2756/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:08,604] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:08,605] [INFO] Selected 19 target genomes.
[2023-03-18 06:03:08,605] [INFO] Target genome list was writen to OceanDNA-b2756/target_genomes.txt
[2023-03-18 06:03:08,827] [INFO] Task started: fastANI
[2023-03-18 06:03:08,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgff567b69-f617-4c94-ab98-49efd616e2e5/OceanDNA-b2756.fa --refList OceanDNA-b2756/target_genomes.txt --output OceanDNA-b2756/fastani_result.tsv --threads 1
[2023-03-18 06:03:18,118] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:18,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:03:18,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:03:18,119] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:03:18,119] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:03:18,119] [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
--------------------------------------------------------------------------------
[2023-03-18 06:03:18,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2756/tc_result.tsv
[2023-03-18 06:03:18,120] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:03:18,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:03:18,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/checkm_data
[2023-03-18 06:03:18,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:03:18,126] [INFO] Task started: CheckM
[2023-03-18 06:03:18,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2756/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2756/checkm_input OceanDNA-b2756/checkm_result
[2023-03-18 06:03:42,198] [INFO] Task succeeded: CheckM
[2023-03-18 06:03:42,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:03:42,200] [INFO] ===== Completeness check finished =====
[2023-03-18 06:03:42,200] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:03:42,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2756/markers.fasta)
[2023-03-18 06:03:42,202] [INFO] Task started: Blastn
[2023-03-18 06:03:42,202] [INFO] Running command: blastn -query OceanDNA-b2756/markers.fasta -db /var/lib/cwl/stga72d65ce-52f1-4f7f-b30a-7aaf0440b6c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2756/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:03:43,072] [INFO] Task succeeded: Blastn
[2023-03-18 06:03:43,073] [INFO] Selected 18 target genomes.
[2023-03-18 06:03:43,073] [INFO] Target genome list was writen to OceanDNA-b2756/target_genomes_gtdb.txt
[2023-03-18 06:03:43,762] [INFO] Task started: fastANI
[2023-03-18 06:03:43,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgff567b69-f617-4c94-ab98-49efd616e2e5/OceanDNA-b2756.fa --refList OceanDNA-b2756/target_genomes_gtdb.txt --output OceanDNA-b2756/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:03:51,455] [INFO] Task succeeded: fastANI
[2023-03-18 06:03:51,459] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:03:51,459] [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_001438965.1	s__Pontimonas sp001438965	99.1719	292	407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	99.36	99.36	0.84	0.84	2	conclusive
GCA_017852615.1	s__Pontimonas sp017852615	78.6711	147	407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	97.57	97.21	0.82	0.78	7	-
GCA_018402295.1	s__Pontimonas sp018402295	78.2887	67	407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704535.1	s__Pontimonas sp009704535	77.8216	71	407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	99.38	99.38	0.88	0.88	2	-
GCA_018666065.1	s__Pontimonas sp018666065	77.7389	85	407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:03:51,459] [INFO] GTDB search result was written to OceanDNA-b2756/result_gtdb.tsv
[2023-03-18 06:03:51,460] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:03:51,460] [INFO] DFAST_QC result json was written to OceanDNA-b2756/dqc_result.json
[2023-03-18 06:03:51,460] [INFO] DFAST_QC completed!
[2023-03-18 06:03:51,460] [INFO] Total running time: 0h0m53s