[2023-03-19 00:33:19,057] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,057] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference
[2023-03-19 00:33:20,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,310] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,311] [INFO] Running command: cat /var/lib/cwl/stg6f9ad1b7-bd85-4700-b625-cfc6938760c7/OceanDNA-b2562.fa | prodigal -d OceanDNA-b2562/cds.fna -a OceanDNA-b2562/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:22,955] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:22,955] [INFO] Task started: HMMsearch
[2023-03-19 00:33:22,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b2562/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/reference_markers.hmm OceanDNA-b2562/protein.faa > /dev/null
[2023-03-19 00:33:23,136] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:23,136] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f9ad1b7-bd85-4700-b625-cfc6938760c7/OceanDNA-b2562.fa]
[2023-03-19 00:33:23,144] [INFO] Query marker FASTA was written to OceanDNA-b2562/markers.fasta
[2023-03-19 00:33:23,144] [INFO] Task started: Blastn
[2023-03-19 00:33:23,144] [INFO] Running command: blastn -query OceanDNA-b2562/markers.fasta -db /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/reference_markers.fasta -out OceanDNA-b2562/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:23,705] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:23,706] [INFO] Selected 23 target genomes.
[2023-03-19 00:33:23,707] [INFO] Target genome list was writen to OceanDNA-b2562/target_genomes.txt
[2023-03-19 00:33:23,724] [INFO] Task started: fastANI
[2023-03-19 00:33:23,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f9ad1b7-bd85-4700-b625-cfc6938760c7/OceanDNA-b2562.fa --refList OceanDNA-b2562/target_genomes.txt --output OceanDNA-b2562/fastani_result.tsv --threads 1
[2023-03-19 00:33:38,128] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:38,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:38,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:38,128] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:38,128] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:38,129] [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
--------------------------------------------------------------------------------
[2023-03-19 00:33:38,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2562/tc_result.tsv
[2023-03-19 00:33:38,129] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:38,129] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:38,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/checkm_data
[2023-03-19 00:33:38,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:38,139] [INFO] Task started: CheckM
[2023-03-19 00:33:38,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2562/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2562/checkm_input OceanDNA-b2562/checkm_result
[2023-03-19 00:33:51,986] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:51,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:33:51,990] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:51,990] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:51,991] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2562/markers.fasta)
[2023-03-19 00:33:51,991] [INFO] Task started: Blastn
[2023-03-19 00:33:51,991] [INFO] Running command: blastn -query OceanDNA-b2562/markers.fasta -db /var/lib/cwl/stg25b4d92f-b26c-4209-8f87-62d5c99b62cc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2562/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:52,829] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:52,831] [INFO] Selected 17 target genomes.
[2023-03-19 00:33:52,831] [INFO] Target genome list was writen to OceanDNA-b2562/target_genomes_gtdb.txt
[2023-03-19 00:33:52,981] [INFO] Task started: fastANI
[2023-03-19 00:33:52,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f9ad1b7-bd85-4700-b625-cfc6938760c7/OceanDNA-b2562.fa --refList OceanDNA-b2562/target_genomes_gtdb.txt --output OceanDNA-b2562/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:33:59,679] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:59,681] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:33:59,682] [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
GCF_000257665.1	s__Aquiluna sp000257665	85.9663	107	115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182225.1	s__Aquiluna sp905182225	84.5694	100	115	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:33:59,682] [INFO] GTDB search result was written to OceanDNA-b2562/result_gtdb.tsv
[2023-03-19 00:33:59,683] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:33:59,684] [INFO] DFAST_QC result json was written to OceanDNA-b2562/dqc_result.json
[2023-03-19 00:33:59,684] [INFO] DFAST_QC completed!
[2023-03-19 00:33:59,684] [INFO] Total running time: 0h0m41s