[2023-03-15 18:12:37,906] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference
[2023-03-15 18:12:39,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,779] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,779] [INFO] Running command: cat /var/lib/cwl/stg266d92c2-f287-4b23-a0c9-26669d91eb18/OceanDNA-b906.fa | prodigal -d OceanDNA-b906/cds.fna -a OceanDNA-b906/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:12:49,299] [INFO] Task succeeded: Prodigal
[2023-03-15 18:12:49,299] [INFO] Task started: HMMsearch
[2023-03-15 18:12:49,299] [INFO] Running command: hmmsearch --tblout OceanDNA-b906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/reference_markers.hmm OceanDNA-b906/protein.faa > /dev/null
[2023-03-15 18:12:49,483] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:12:49,484] [INFO] Found 6/6 markers.
[2023-03-15 18:12:49,497] [INFO] Query marker FASTA was written to OceanDNA-b906/markers.fasta
[2023-03-15 18:12:49,497] [INFO] Task started: Blastn
[2023-03-15 18:12:49,497] [INFO] Running command: blastn -query OceanDNA-b906/markers.fasta -db /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/reference_markers.fasta -out OceanDNA-b906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:12:50,070] [INFO] Task succeeded: Blastn
[2023-03-15 18:12:50,071] [INFO] Selected 19 target genomes.
[2023-03-15 18:12:50,072] [INFO] Target genome list was writen to OceanDNA-b906/target_genomes.txt
[2023-03-15 18:12:50,246] [INFO] Task started: fastANI
[2023-03-15 18:12:50,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg266d92c2-f287-4b23-a0c9-26669d91eb18/OceanDNA-b906.fa --refList OceanDNA-b906/target_genomes.txt --output OceanDNA-b906/fastani_result.tsv --threads 1
[2023-03-15 18:12:57,567] [INFO] Task succeeded: fastANI
[2023-03-15 18:12:57,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:12:57,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:12:57,568] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:12:57,568] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:12:57,568] [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 18:12:57,568] [INFO] DFAST Taxonomy check result was written to OceanDNA-b906/tc_result.tsv
[2023-03-15 18:12:57,568] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:12:57,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:12:57,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/checkm_data
[2023-03-15 18:12:57,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:12:57,575] [INFO] Task started: CheckM
[2023-03-15 18:12:57,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b906/checkm_input OceanDNA-b906/checkm_result
[2023-03-15 18:13:26,017] [INFO] Task succeeded: CheckM
[2023-03-15 18:13:26,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:13:26,019] [INFO] ===== Completeness check finished =====
[2023-03-15 18:13:26,019] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:13:26,019] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b906/markers.fasta)
[2023-03-15 18:13:26,020] [INFO] Task started: Blastn
[2023-03-15 18:13:26,020] [INFO] Running command: blastn -query OceanDNA-b906/markers.fasta -db /var/lib/cwl/stgff80285f-09b5-4731-b629-225adcd30d29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:26,968] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:26,968] [INFO] Selected 22 target genomes.
[2023-03-15 18:13:26,969] [INFO] Target genome list was writen to OceanDNA-b906/target_genomes_gtdb.txt
[2023-03-15 18:13:27,137] [INFO] Task started: fastANI
[2023-03-15 18:13:27,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg266d92c2-f287-4b23-a0c9-26669d91eb18/OceanDNA-b906.fa --refList OceanDNA-b906/target_genomes_gtdb.txt --output OceanDNA-b906/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:13:34,172] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:34,175] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:13:34,175] [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_000817115.1	s__MedAcidi-G2B sp000817115	99.8556	451	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902634555.1	s__MedAcidi-G2B sp902634555	90.0155	333	570	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:13:34,175] [INFO] GTDB search result was written to OceanDNA-b906/result_gtdb.tsv
[2023-03-15 18:13:34,175] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:13:34,176] [INFO] DFAST_QC result json was written to OceanDNA-b906/dqc_result.json
[2023-03-15 18:13:34,176] [INFO] DFAST_QC completed!
[2023-03-15 18:13:34,176] [INFO] Total running time: 0h0m56s