[2023-03-15 21:57:40,345] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:57:40,345] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:57:40,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference
[2023-03-15 21:57:41,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:57:41,435] [INFO] Task started: Prodigal
[2023-03-15 21:57:41,436] [INFO] Running command: cat /var/lib/cwl/stgc3233028-2731-40a2-ac82-248074f0b009/OceanDNA-b103.fa | prodigal -d OceanDNA-b103/cds.fna -a OceanDNA-b103/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:57:55,006] [INFO] Task succeeded: Prodigal
[2023-03-15 21:57:55,006] [INFO] Task started: HMMsearch
[2023-03-15 21:57:55,006] [INFO] Running command: hmmsearch --tblout OceanDNA-b103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/reference_markers.hmm OceanDNA-b103/protein.faa > /dev/null
[2023-03-15 21:57:55,186] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:57:55,186] [INFO] Found 6/6 markers.
[2023-03-15 21:57:55,218] [INFO] Query marker FASTA was written to OceanDNA-b103/markers.fasta
[2023-03-15 21:57:55,218] [INFO] Task started: Blastn
[2023-03-15 21:57:55,218] [INFO] Running command: blastn -query OceanDNA-b103/markers.fasta -db /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/reference_markers.fasta -out OceanDNA-b103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:57:55,737] [INFO] Task succeeded: Blastn
[2023-03-15 21:57:55,747] [INFO] Selected 13 target genomes.
[2023-03-15 21:57:55,747] [INFO] Target genome list was writen to OceanDNA-b103/target_genomes.txt
[2023-03-15 21:57:55,754] [INFO] Task started: fastANI
[2023-03-15 21:57:55,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3233028-2731-40a2-ac82-248074f0b009/OceanDNA-b103.fa --refList OceanDNA-b103/target_genomes.txt --output OceanDNA-b103/fastani_result.tsv --threads 1
[2023-03-15 21:58:04,270] [INFO] Task succeeded: fastANI
[2023-03-15 21:58:04,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:58:04,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:58:04,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:58:04,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:58:04,271] [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 21:58:04,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b103/tc_result.tsv
[2023-03-15 21:58:04,280] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:58:04,280] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:58:04,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/checkm_data
[2023-03-15 21:58:04,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:58:04,321] [INFO] Task started: CheckM
[2023-03-15 21:58:04,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b103/checkm_input OceanDNA-b103/checkm_result
[2023-03-15 21:58:41,653] [INFO] Task succeeded: CheckM
[2023-03-15 21:58:41,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:58:41,784] [INFO] ===== Completeness check finished =====
[2023-03-15 21:58:41,784] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:58:41,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b103/markers.fasta)
[2023-03-15 21:58:41,784] [INFO] Task started: Blastn
[2023-03-15 21:58:41,784] [INFO] Running command: blastn -query OceanDNA-b103/markers.fasta -db /var/lib/cwl/stg7ddbbd8e-72bb-4e90-aef2-336d03e005d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:58:42,534] [INFO] Task succeeded: Blastn
[2023-03-15 21:58:42,542] [INFO] Selected 21 target genomes.
[2023-03-15 21:58:42,543] [INFO] Target genome list was writen to OceanDNA-b103/target_genomes_gtdb.txt
[2023-03-15 21:58:43,043] [INFO] Task started: fastANI
[2023-03-15 21:58:43,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3233028-2731-40a2-ac82-248074f0b009/OceanDNA-b103.fa --refList OceanDNA-b103/target_genomes_gtdb.txt --output OceanDNA-b103/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:58:53,482] [INFO] Task succeeded: fastANI
[2023-03-15 21:58:53,484] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:58:53,484] [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_002722645.1	s__UBA890 sp002722645	95.1333	587	729	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	97.90	97.61	0.78	0.75	3	conclusive
GCA_002731215.1	s__UBA890 sp002731215	88.2569	272	729	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:58:53,487] [INFO] GTDB search result was written to OceanDNA-b103/result_gtdb.tsv
[2023-03-15 21:58:53,493] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:58:53,498] [INFO] DFAST_QC result json was written to OceanDNA-b103/dqc_result.json
[2023-03-15 21:58:53,498] [INFO] DFAST_QC completed!
[2023-03-15 21:58:53,498] [INFO] Total running time: 0h1m13s