[2023-03-19 03:50:09,625] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:09,625] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:09,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference
[2023-03-19 03:50:10,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:10,718] [INFO] Task started: Prodigal
[2023-03-19 03:50:10,718] [INFO] Running command: cat /var/lib/cwl/stgaa1c54ac-149d-4602-a3a3-20ba7117de86/OceanDNA-b19055.fa | prodigal -d OceanDNA-b19055/cds.fna -a OceanDNA-b19055/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:16,521] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:16,521] [INFO] Task started: HMMsearch
[2023-03-19 03:50:16,521] [INFO] Running command: hmmsearch --tblout OceanDNA-b19055/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/reference_markers.hmm OceanDNA-b19055/protein.faa > /dev/null
[2023-03-19 03:50:16,701] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:16,701] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaa1c54ac-149d-4602-a3a3-20ba7117de86/OceanDNA-b19055.fa]
[2023-03-19 03:50:16,713] [INFO] Query marker FASTA was written to OceanDNA-b19055/markers.fasta
[2023-03-19 03:50:16,713] [INFO] Task started: Blastn
[2023-03-19 03:50:16,713] [INFO] Running command: blastn -query OceanDNA-b19055/markers.fasta -db /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/reference_markers.fasta -out OceanDNA-b19055/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:17,215] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:17,215] [INFO] Selected 21 target genomes.
[2023-03-19 03:50:17,216] [INFO] Target genome list was writen to OceanDNA-b19055/target_genomes.txt
[2023-03-19 03:50:17,226] [INFO] Task started: fastANI
[2023-03-19 03:50:17,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa1c54ac-149d-4602-a3a3-20ba7117de86/OceanDNA-b19055.fa --refList OceanDNA-b19055/target_genomes.txt --output OceanDNA-b19055/fastani_result.tsv --threads 1
[2023-03-19 03:50:25,328] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:25,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:25,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:25,328] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:25,328] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:25,329] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:25,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19055/tc_result.tsv
[2023-03-19 03:50:25,329] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:25,329] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:25,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/checkm_data
[2023-03-19 03:50:25,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:25,334] [INFO] Task started: CheckM
[2023-03-19 03:50:25,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19055/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19055/checkm_input OceanDNA-b19055/checkm_result
[2023-03-19 03:50:45,812] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:45,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:45,815] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:45,815] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:45,815] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19055/markers.fasta)
[2023-03-19 03:50:45,815] [INFO] Task started: Blastn
[2023-03-19 03:50:45,815] [INFO] Running command: blastn -query OceanDNA-b19055/markers.fasta -db /var/lib/cwl/stg33e56cac-f0f9-4de1-a27a-192b3c28ac3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19055/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:46,534] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:46,535] [INFO] Selected 24 target genomes.
[2023-03-19 03:50:46,535] [INFO] Target genome list was writen to OceanDNA-b19055/target_genomes_gtdb.txt
[2023-03-19 03:50:46,559] [INFO] Task started: fastANI
[2023-03-19 03:50:46,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa1c54ac-149d-4602-a3a3-20ba7117de86/OceanDNA-b19055.fa --refList OceanDNA-b19055/target_genomes_gtdb.txt --output OceanDNA-b19055/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:53,874] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:53,876] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:50:53,877] [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_905182385.1	s__TCS55 sp905182385	98.9171	282	371	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239505.1	s__TCS55 sp014239505	82.7341	249	371	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	98.16	97.99	0.75	0.73	6	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:53,877] [INFO] GTDB search result was written to OceanDNA-b19055/result_gtdb.tsv
[2023-03-19 03:50:53,877] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:53,877] [INFO] DFAST_QC result json was written to OceanDNA-b19055/dqc_result.json
[2023-03-19 03:50:53,877] [INFO] DFAST_QC completed!
[2023-03-19 03:50:53,878] [INFO] Total running time: 0h0m44s