[2023-03-18 22:09:38,387] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:09:38,387] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:09:38,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference
[2023-03-18 22:09:40,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:09:40,574] [INFO] Task started: Prodigal
[2023-03-18 22:09:40,574] [INFO] Running command: cat /var/lib/cwl/stg2adf9553-db49-44a5-aa41-3d2112b0c38b/OceanDNA-a1485.fa | prodigal -d OceanDNA-a1485/cds.fna -a OceanDNA-a1485/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:09:45,146] [INFO] Task succeeded: Prodigal
[2023-03-18 22:09:45,146] [INFO] Task started: HMMsearch
[2023-03-18 22:09:45,146] [INFO] Running command: hmmsearch --tblout OceanDNA-a1485/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/reference_markers.hmm OceanDNA-a1485/protein.faa > /dev/null
[2023-03-18 22:09:45,281] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:09:45,281] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2adf9553-db49-44a5-aa41-3d2112b0c38b/OceanDNA-a1485.fa]
[2023-03-18 22:09:45,288] [INFO] Query marker FASTA was written to OceanDNA-a1485/markers.fasta
[2023-03-18 22:09:45,288] [INFO] Task started: Blastn
[2023-03-18 22:09:45,288] [INFO] Running command: blastn -query OceanDNA-a1485/markers.fasta -db /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/reference_markers.fasta -out OceanDNA-a1485/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:09:47,557] [INFO] Task succeeded: Blastn
[2023-03-18 22:09:47,558] [INFO] Selected 10 target genomes.
[2023-03-18 22:09:47,558] [INFO] Target genome list was writen to OceanDNA-a1485/target_genomes.txt
[2023-03-18 22:09:47,568] [INFO] Task started: fastANI
[2023-03-18 22:09:47,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg2adf9553-db49-44a5-aa41-3d2112b0c38b/OceanDNA-a1485.fa --refList OceanDNA-a1485/target_genomes.txt --output OceanDNA-a1485/fastani_result.tsv --threads 1
[2023-03-18 22:09:52,965] [INFO] Task succeeded: fastANI
[2023-03-18 22:09:52,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:09:52,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:09:52,966] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:09:52,966] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:09:52,966] [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 22:09:52,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1485/tc_result.tsv
[2023-03-18 22:09:52,966] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:09:52,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:09:52,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/checkm_data
[2023-03-18 22:09:52,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:09:52,971] [INFO] Task started: CheckM
[2023-03-18 22:09:52,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1485/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1485/checkm_input OceanDNA-a1485/checkm_result
[2023-03-18 22:10:11,294] [INFO] Task succeeded: CheckM
[2023-03-18 22:10:11,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:10:11,296] [INFO] ===== Completeness check finished =====
[2023-03-18 22:10:11,296] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:10:11,296] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1485/markers.fasta)
[2023-03-18 22:10:11,297] [INFO] Task started: Blastn
[2023-03-18 22:10:11,297] [INFO] Running command: blastn -query OceanDNA-a1485/markers.fasta -db /var/lib/cwl/stg312bd2c2-f76c-43fb-96f3-1b1cabbbf16e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1485/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:11,872] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:11,873] [INFO] Selected 9 target genomes.
[2023-03-18 22:10:11,873] [INFO] Target genome list was writen to OceanDNA-a1485/target_genomes_gtdb.txt
[2023-03-18 22:10:11,884] [INFO] Task started: fastANI
[2023-03-18 22:10:11,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg2adf9553-db49-44a5-aa41-3d2112b0c38b/OceanDNA-a1485.fa --refList OceanDNA-a1485/target_genomes_gtdb.txt --output OceanDNA-a1485/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:10:14,455] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:14,457] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:10:14,457] [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_002688315.1	s__UBA492 sp002688315	99.9037	251	274	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__UBA10216;g__UBA492	95.0	99.92	99.91	0.97	0.97	3	conclusive
--------------------------------------------------------------------------------
[2023-03-18 22:10:14,457] [INFO] GTDB search result was written to OceanDNA-a1485/result_gtdb.tsv
[2023-03-18 22:10:14,457] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:10:14,458] [INFO] DFAST_QC result json was written to OceanDNA-a1485/dqc_result.json
[2023-03-18 22:10:14,458] [INFO] DFAST_QC completed!
[2023-03-18 22:10:14,458] [INFO] Total running time: 0h0m36s