[2023-03-15 06:50:51,576] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:50:51,589] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:50:51,589] [INFO] DQC Reference Directory: /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference
[2023-03-15 06:50:53,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:50:53,468] [INFO] Task started: Prodigal
[2023-03-15 06:50:53,469] [INFO] Running command: cat /var/lib/cwl/stg3cba7e25-1320-4921-9598-7c95d2223b96/OceanDNA-b26108.fa | prodigal -d OceanDNA-b26108/cds.fna -a OceanDNA-b26108/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:50:57,715] [INFO] Task succeeded: Prodigal
[2023-03-15 06:50:57,716] [INFO] Task started: HMMsearch
[2023-03-15 06:50:57,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b26108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/reference_markers.hmm OceanDNA-b26108/protein.faa > /dev/null
[2023-03-15 06:50:57,870] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:50:57,871] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3cba7e25-1320-4921-9598-7c95d2223b96/OceanDNA-b26108.fa]
[2023-03-15 06:50:58,019] [INFO] Query marker FASTA was written to OceanDNA-b26108/markers.fasta
[2023-03-15 06:50:58,020] [INFO] Task started: Blastn
[2023-03-15 06:50:58,020] [INFO] Running command: blastn -query OceanDNA-b26108/markers.fasta -db /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/reference_markers.fasta -out OceanDNA-b26108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:50:59,655] [INFO] Task succeeded: Blastn
[2023-03-15 06:50:59,688] [INFO] Selected 23 target genomes.
[2023-03-15 06:50:59,688] [INFO] Target genome list was writen to OceanDNA-b26108/target_genomes.txt
[2023-03-15 06:50:59,806] [INFO] Task started: fastANI
[2023-03-15 06:50:59,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cba7e25-1320-4921-9598-7c95d2223b96/OceanDNA-b26108.fa --refList OceanDNA-b26108/target_genomes.txt --output OceanDNA-b26108/fastani_result.tsv --threads 1
[2023-03-15 06:51:14,421] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:14,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:51:14,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:51:14,422] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:51:14,422] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:51:14,422] [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
--------------------------------------------------------------------------------
[2023-03-15 06:51:14,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26108/tc_result.tsv
[2023-03-15 06:51:14,471] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:51:14,471] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:51:14,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/checkm_data
[2023-03-15 06:51:14,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:51:14,526] [INFO] Task started: CheckM
[2023-03-15 06:51:14,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26108/checkm_input OceanDNA-b26108/checkm_result
[2023-03-15 06:51:32,086] [INFO] Task succeeded: CheckM
[2023-03-15 06:51:32,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.15%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 06:51:32,274] [INFO] ===== Completeness check finished =====
[2023-03-15 06:51:32,275] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:51:32,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26108/markers.fasta)
[2023-03-15 06:51:32,276] [INFO] Task started: Blastn
[2023-03-15 06:51:32,276] [INFO] Running command: blastn -query OceanDNA-b26108/markers.fasta -db /var/lib/cwl/stge4d2d7e3-805d-418e-afb1-88072fc743f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:33,218] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:33,250] [INFO] Selected 25 target genomes.
[2023-03-15 06:51:33,250] [INFO] Target genome list was writen to OceanDNA-b26108/target_genomes_gtdb.txt
[2023-03-15 06:51:33,371] [INFO] Task started: fastANI
[2023-03-15 06:51:33,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cba7e25-1320-4921-9598-7c95d2223b96/OceanDNA-b26108.fa --refList OceanDNA-b26108/target_genomes_gtdb.txt --output OceanDNA-b26108/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:51:41,478] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:41,480] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:51:41,480] [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_016780775.1	s__JADHLI01 sp016780775	78.6382	74	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLI01	95.0	99.93	99.93	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:51:41,480] [INFO] GTDB search result was written to OceanDNA-b26108/result_gtdb.tsv
[2023-03-15 06:51:41,480] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:51:41,481] [INFO] DFAST_QC result json was written to OceanDNA-b26108/dqc_result.json
[2023-03-15 06:51:41,481] [INFO] DFAST_QC completed!
[2023-03-15 06:51:41,481] [INFO] Total running time: 0h0m50s