[2023-03-18 09:19:06,954] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:19:06,956] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:19:06,957] [INFO] DQC Reference Directory: /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference
[2023-03-18 09:19:08,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:19:08,109] [INFO] Task started: Prodigal
[2023-03-18 09:19:08,109] [INFO] Running command: cat /var/lib/cwl/stgdca4724b-8b40-481e-8637-7754e34ae0be/OceanDNA-b18804.fa | prodigal -d OceanDNA-b18804/cds.fna -a OceanDNA-b18804/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:19:13,452] [INFO] Task succeeded: Prodigal
[2023-03-18 09:19:13,452] [INFO] Task started: HMMsearch
[2023-03-18 09:19:13,452] [INFO] Running command: hmmsearch --tblout OceanDNA-b18804/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/reference_markers.hmm OceanDNA-b18804/protein.faa > /dev/null
[2023-03-18 09:19:13,611] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:19:13,612] [INFO] Found 6/6 markers.
[2023-03-18 09:19:13,643] [INFO] Query marker FASTA was written to OceanDNA-b18804/markers.fasta
[2023-03-18 09:19:13,645] [INFO] Task started: Blastn
[2023-03-18 09:19:13,645] [INFO] Running command: blastn -query OceanDNA-b18804/markers.fasta -db /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/reference_markers.fasta -out OceanDNA-b18804/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:19:14,155] [INFO] Task succeeded: Blastn
[2023-03-18 09:19:14,165] [INFO] Selected 21 target genomes.
[2023-03-18 09:19:14,165] [INFO] Target genome list was writen to OceanDNA-b18804/target_genomes.txt
[2023-03-18 09:19:14,177] [INFO] Task started: fastANI
[2023-03-18 09:19:14,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca4724b-8b40-481e-8637-7754e34ae0be/OceanDNA-b18804.fa --refList OceanDNA-b18804/target_genomes.txt --output OceanDNA-b18804/fastani_result.tsv --threads 1
[2023-03-18 09:19:24,267] [INFO] Task succeeded: fastANI
[2023-03-18 09:19:24,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:19:24,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:19:24,268] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:19:24,268] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:19:24,268] [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 09:19:24,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18804/tc_result.tsv
[2023-03-18 09:19:24,272] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:19:24,272] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:19:24,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/checkm_data
[2023-03-18 09:19:24,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:19:24,280] [INFO] Task started: CheckM
[2023-03-18 09:19:24,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18804/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18804/checkm_input OceanDNA-b18804/checkm_result
[2023-03-18 09:19:43,617] [INFO] Task succeeded: CheckM
[2023-03-18 09:19:43,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.95%
Contamintation: 3.45%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:19:43,644] [INFO] ===== Completeness check finished =====
[2023-03-18 09:19:43,644] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:19:43,644] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18804/markers.fasta)
[2023-03-18 09:19:43,646] [INFO] Task started: Blastn
[2023-03-18 09:19:43,646] [INFO] Running command: blastn -query OceanDNA-b18804/markers.fasta -db /var/lib/cwl/stgd06b41ec-30ea-46e4-8805-2d756fb8ffcb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18804/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:19:44,359] [INFO] Task succeeded: Blastn
[2023-03-18 09:19:44,364] [INFO] Selected 26 target genomes.
[2023-03-18 09:19:44,364] [INFO] Target genome list was writen to OceanDNA-b18804/target_genomes_gtdb.txt
[2023-03-18 09:19:44,533] [INFO] Task started: fastANI
[2023-03-18 09:19:44,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca4724b-8b40-481e-8637-7754e34ae0be/OceanDNA-b18804.fa --refList OceanDNA-b18804/target_genomes_gtdb.txt --output OceanDNA-b18804/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:19:52,749] [INFO] Task succeeded: fastANI
[2023-03-18 09:19:52,752] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:19:52,752] [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_002713455.1	s__GCA-002713455 sp002713455	98.6539	253	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002713455	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902581045.1	s__GCA-002713455 sp902581045	83.1843	146	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002713455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182385.1	s__TCS55 sp905182385	76.4449	51	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:19:52,753] [INFO] GTDB search result was written to OceanDNA-b18804/result_gtdb.tsv
[2023-03-18 09:19:52,758] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:19:52,760] [INFO] DFAST_QC result json was written to OceanDNA-b18804/dqc_result.json
[2023-03-18 09:19:52,761] [INFO] DFAST_QC completed!
[2023-03-18 09:19:52,761] [INFO] Total running time: 0h0m46s