[2023-03-18 02:01:38,623] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:01:38,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:01:38,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference
[2023-03-18 02:01:39,762] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:01:39,763] [INFO] Task started: Prodigal
[2023-03-18 02:01:39,763] [INFO] Running command: cat /var/lib/cwl/stg4baa2c4a-0704-47a0-a7a6-615fd281d61e/OceanDNA-a1123.fa | prodigal -d OceanDNA-a1123/cds.fna -a OceanDNA-a1123/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:01:42,043] [INFO] Task succeeded: Prodigal
[2023-03-18 02:01:42,043] [INFO] Task started: HMMsearch
[2023-03-18 02:01:42,043] [INFO] Running command: hmmsearch --tblout OceanDNA-a1123/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/reference_markers.hmm OceanDNA-a1123/protein.faa > /dev/null
[2023-03-18 02:01:42,157] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:01:42,158] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4baa2c4a-0704-47a0-a7a6-615fd281d61e/OceanDNA-a1123.fa]
[2023-03-18 02:01:42,161] [INFO] Query marker FASTA was written to OceanDNA-a1123/markers.fasta
[2023-03-18 02:01:42,162] [INFO] Task started: Blastn
[2023-03-18 02:01:42,163] [INFO] Running command: blastn -query OceanDNA-a1123/markers.fasta -db /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/reference_markers.fasta -out OceanDNA-a1123/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:01:42,666] [INFO] Task succeeded: Blastn
[2023-03-18 02:01:42,667] [INFO] Selected 5 target genomes.
[2023-03-18 02:01:42,667] [INFO] Target genome list was writen to OceanDNA-a1123/target_genomes.txt
[2023-03-18 02:01:42,673] [INFO] Task started: fastANI
[2023-03-18 02:01:42,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg4baa2c4a-0704-47a0-a7a6-615fd281d61e/OceanDNA-a1123.fa --refList OceanDNA-a1123/target_genomes.txt --output OceanDNA-a1123/fastani_result.tsv --threads 1
[2023-03-18 02:01:45,786] [INFO] Task succeeded: fastANI
[2023-03-18 02:01:45,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:01:45,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:01:45,787] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:01:45,787] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:01:45,787] [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 02:01:45,787] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1123/tc_result.tsv
[2023-03-18 02:01:45,787] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:01:45,787] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:01:45,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/checkm_data
[2023-03-18 02:01:45,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:01:45,799] [INFO] Task started: CheckM
[2023-03-18 02:01:45,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1123/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1123/checkm_input OceanDNA-a1123/checkm_result
[2023-03-18 02:01:58,166] [INFO] Task succeeded: CheckM
[2023-03-18 02:01:58,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:01:58,167] [INFO] ===== Completeness check finished =====
[2023-03-18 02:01:58,167] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:01:58,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1123/markers.fasta)
[2023-03-18 02:01:58,168] [INFO] Task started: Blastn
[2023-03-18 02:01:58,169] [INFO] Running command: blastn -query OceanDNA-a1123/markers.fasta -db /var/lib/cwl/stg6a3390db-6695-4c43-90a1-e955a5005af2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1123/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:01:58,901] [INFO] Task succeeded: Blastn
[2023-03-18 02:01:58,902] [INFO] Selected 9 target genomes.
[2023-03-18 02:01:58,902] [INFO] Target genome list was writen to OceanDNA-a1123/target_genomes_gtdb.txt
[2023-03-18 02:01:58,907] [INFO] Task started: fastANI
[2023-03-18 02:01:58,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg4baa2c4a-0704-47a0-a7a6-615fd281d61e/OceanDNA-a1123.fa --refList OceanDNA-a1123/target_genomes_gtdb.txt --output OceanDNA-a1123/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:02:00,027] [INFO] Task succeeded: fastANI
[2023-03-18 02:02:00,029] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:02:00,029] [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_002731115.1	s__NP1466 sp002731115	99.9008	105	129	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__NP1466	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 02:02:00,030] [INFO] GTDB search result was written to OceanDNA-a1123/result_gtdb.tsv
[2023-03-18 02:02:00,030] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:02:00,030] [INFO] DFAST_QC result json was written to OceanDNA-a1123/dqc_result.json
[2023-03-18 02:02:00,030] [INFO] DFAST_QC completed!
[2023-03-18 02:02:00,030] [INFO] Total running time: 0h0m21s