[2023-03-18 00:21:54,211] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,212] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference
[2023-03-18 00:21:55,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,650] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stgf6f19ae8-2a7b-46d0-9b95-893f15640fc8/OceanDNA-b31170.fa | prodigal -d OceanDNA-b31170/cds.fna -a OceanDNA-b31170/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:09,163] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:09,163] [INFO] Task started: HMMsearch
[2023-03-18 00:22:09,163] [INFO] Running command: hmmsearch --tblout OceanDNA-b31170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/reference_markers.hmm OceanDNA-b31170/protein.faa > /dev/null
[2023-03-18 00:22:09,345] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:09,345] [INFO] Found 6/6 markers.
[2023-03-18 00:22:09,370] [INFO] Query marker FASTA was written to OceanDNA-b31170/markers.fasta
[2023-03-18 00:22:09,371] [INFO] Task started: Blastn
[2023-03-18 00:22:09,371] [INFO] Running command: blastn -query OceanDNA-b31170/markers.fasta -db /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/reference_markers.fasta -out OceanDNA-b31170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:09,964] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:09,966] [INFO] Selected 25 target genomes.
[2023-03-18 00:22:09,966] [INFO] Target genome list was writen to OceanDNA-b31170/target_genomes.txt
[2023-03-18 00:22:09,978] [INFO] Task started: fastANI
[2023-03-18 00:22:09,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f19ae8-2a7b-46d0-9b95-893f15640fc8/OceanDNA-b31170.fa --refList OceanDNA-b31170/target_genomes.txt --output OceanDNA-b31170/fastani_result.tsv --threads 1
[2023-03-18 00:22:25,575] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:25,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:25,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:25,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:25,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:25,576] [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 00:22:25,576] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31170/tc_result.tsv
[2023-03-18 00:22:25,577] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:25,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:25,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/checkm_data
[2023-03-18 00:22:25,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:25,584] [INFO] Task started: CheckM
[2023-03-18 00:22:25,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31170/checkm_input OceanDNA-b31170/checkm_result
[2023-03-18 00:23:02,923] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:02,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 1.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:02,926] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:02,927] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:02,927] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31170/markers.fasta)
[2023-03-18 00:23:02,927] [INFO] Task started: Blastn
[2023-03-18 00:23:02,927] [INFO] Running command: blastn -query OceanDNA-b31170/markers.fasta -db /var/lib/cwl/stg26526000-5c5e-4510-91fa-dfe077e9c850/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:03,918] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:03,919] [INFO] Selected 20 target genomes.
[2023-03-18 00:23:03,919] [INFO] Target genome list was writen to OceanDNA-b31170/target_genomes_gtdb.txt
[2023-03-18 00:23:03,964] [INFO] Task started: fastANI
[2023-03-18 00:23:03,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6f19ae8-2a7b-46d0-9b95-893f15640fc8/OceanDNA-b31170.fa --refList OceanDNA-b31170/target_genomes_gtdb.txt --output OceanDNA-b31170/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:16,289] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:16,292] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:23:16,292] [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_018649245.1	s__UBA2165 sp018649245	98.8105	436	698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	99.23	99.23	0.84	0.84	2	conclusive
GCA_002327565.1	s__UBA2165 sp002327565	82.4104	519	698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018649725.1	s__TMED23 sp018649725	79.0055	259	698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	99.78	99.75	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:16,292] [INFO] GTDB search result was written to OceanDNA-b31170/result_gtdb.tsv
[2023-03-18 00:23:16,292] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:16,293] [INFO] DFAST_QC result json was written to OceanDNA-b31170/dqc_result.json
[2023-03-18 00:23:16,293] [INFO] DFAST_QC completed!
[2023-03-18 00:23:16,293] [INFO] Total running time: 0h1m22s