[2023-03-16 17:31:39,750] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:31:39,750] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:31:39,750] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference
[2023-03-16 17:31:42,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:31:42,128] [INFO] Task started: Prodigal
[2023-03-16 17:31:42,129] [INFO] Running command: cat /var/lib/cwl/stgb5341334-9580-46d2-8c9e-0de4b208623c/OceanDNA-b24818.fa | prodigal -d OceanDNA-b24818/cds.fna -a OceanDNA-b24818/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:31:56,635] [INFO] Task succeeded: Prodigal
[2023-03-16 17:31:56,636] [INFO] Task started: HMMsearch
[2023-03-16 17:31:56,636] [INFO] Running command: hmmsearch --tblout OceanDNA-b24818/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/reference_markers.hmm OceanDNA-b24818/protein.faa > /dev/null
[2023-03-16 17:31:56,823] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:31:56,823] [INFO] Found 6/6 markers.
[2023-03-16 17:31:56,845] [INFO] Query marker FASTA was written to OceanDNA-b24818/markers.fasta
[2023-03-16 17:31:56,847] [INFO] Task started: Blastn
[2023-03-16 17:31:56,847] [INFO] Running command: blastn -query OceanDNA-b24818/markers.fasta -db /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/reference_markers.fasta -out OceanDNA-b24818/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:31:57,399] [INFO] Task succeeded: Blastn
[2023-03-16 17:31:57,401] [INFO] Selected 15 target genomes.
[2023-03-16 17:31:57,401] [INFO] Target genome list was writen to OceanDNA-b24818/target_genomes.txt
[2023-03-16 17:31:57,412] [INFO] Task started: fastANI
[2023-03-16 17:31:57,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5341334-9580-46d2-8c9e-0de4b208623c/OceanDNA-b24818.fa --refList OceanDNA-b24818/target_genomes.txt --output OceanDNA-b24818/fastani_result.tsv --threads 1
[2023-03-16 17:32:04,319] [INFO] Task succeeded: fastANI
[2023-03-16 17:32:04,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:32:04,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:32:04,319] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:32:04,319] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:32:04,319] [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
--------------------------------------------------------------------------------
[2023-03-16 17:32:04,321] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24818/tc_result.tsv
[2023-03-16 17:32:04,321] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:32:04,321] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:32:04,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/checkm_data
[2023-03-16 17:32:04,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:32:04,330] [INFO] Task started: CheckM
[2023-03-16 17:32:04,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24818/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24818/checkm_input OceanDNA-b24818/checkm_result
[2023-03-16 17:32:49,592] [INFO] Task succeeded: CheckM
[2023-03-16 17:32:49,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:32:49,595] [INFO] ===== Completeness check finished =====
[2023-03-16 17:32:49,595] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:32:49,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24818/markers.fasta)
[2023-03-16 17:32:49,596] [INFO] Task started: Blastn
[2023-03-16 17:32:49,596] [INFO] Running command: blastn -query OceanDNA-b24818/markers.fasta -db /var/lib/cwl/stgcd2b4cde-2620-4dcd-897c-e794acf1aa29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24818/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:32:50,473] [INFO] Task succeeded: Blastn
[2023-03-16 17:32:50,473] [INFO] Selected 26 target genomes.
[2023-03-16 17:32:50,473] [INFO] Target genome list was writen to OceanDNA-b24818/target_genomes_gtdb.txt
[2023-03-16 17:32:50,505] [INFO] Task started: fastANI
[2023-03-16 17:32:50,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5341334-9580-46d2-8c9e-0de4b208623c/OceanDNA-b24818.fa --refList OceanDNA-b24818/target_genomes_gtdb.txt --output OceanDNA-b24818/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:32:58,062] [INFO] Task succeeded: fastANI
[2023-03-16 17:32:58,065] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:32:58,065] [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_002708305.1	s__UBA7326 sp002708305	98.224	669	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	98.40	98.02	0.79	0.75	5	conclusive
GCA_003284265.1	s__UBA7326 sp003284265	77.4245	142	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002709155.1	s__UBA7326 sp002709155	76.8516	92	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:32:58,066] [INFO] GTDB search result was written to OceanDNA-b24818/result_gtdb.tsv
[2023-03-16 17:32:58,066] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:32:58,066] [INFO] DFAST_QC result json was written to OceanDNA-b24818/dqc_result.json
[2023-03-16 17:32:58,066] [INFO] DFAST_QC completed!
[2023-03-16 17:32:58,066] [INFO] Total running time: 0h1m18s