[2023-03-15 07:29:11,755] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,589] [INFO] Running command: cat /var/lib/cwl/stg87865cdf-d43e-4179-88c3-47b7ed59f56d/OceanDNA-a1050.fa | prodigal -d OceanDNA-a1050/cds.fna -a OceanDNA-a1050/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:17,689] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:17,690] [INFO] Task started: HMMsearch
[2023-03-15 07:29:17,690] [INFO] Running command: hmmsearch --tblout OceanDNA-a1050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/reference_markers.hmm OceanDNA-a1050/protein.faa > /dev/null
[2023-03-15 07:29:17,816] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:17,817] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg87865cdf-d43e-4179-88c3-47b7ed59f56d/OceanDNA-a1050.fa]
[2023-03-15 07:29:17,822] [INFO] Query marker FASTA was written to OceanDNA-a1050/markers.fasta
[2023-03-15 07:29:17,822] [INFO] Task started: Blastn
[2023-03-15 07:29:17,822] [INFO] Running command: blastn -query OceanDNA-a1050/markers.fasta -db /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/reference_markers.fasta -out OceanDNA-a1050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:19,024] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:19,025] [INFO] Selected 5 target genomes.
[2023-03-15 07:29:19,025] [INFO] Target genome list was writen to OceanDNA-a1050/target_genomes.txt
[2023-03-15 07:29:19,029] [INFO] Task started: fastANI
[2023-03-15 07:29:19,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg87865cdf-d43e-4179-88c3-47b7ed59f56d/OceanDNA-a1050.fa --refList OceanDNA-a1050/target_genomes.txt --output OceanDNA-a1050/fastani_result.tsv --threads 1
[2023-03-15 07:29:20,656] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:20,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:20,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:20,657] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:20,657] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:20,657] [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 07:29:20,657] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1050/tc_result.tsv
[2023-03-15 07:29:20,657] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:20,657] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:20,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/checkm_data
[2023-03-15 07:29:20,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:20,662] [INFO] Task started: CheckM
[2023-03-15 07:29:20,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1050/checkm_input OceanDNA-a1050/checkm_result
[2023-03-15 07:29:37,688] [INFO] Task succeeded: CheckM
[2023-03-15 07:29:37,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:29:37,689] [INFO] ===== Completeness check finished =====
[2023-03-15 07:29:37,690] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:29:37,690] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1050/markers.fasta)
[2023-03-15 07:29:37,690] [INFO] Task started: Blastn
[2023-03-15 07:29:37,690] [INFO] Running command: blastn -query OceanDNA-a1050/markers.fasta -db /var/lib/cwl/stg040525c2-7f1e-4047-9b0e-d6ffa967ca6c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:38,271] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:38,271] [INFO] Selected 7 target genomes.
[2023-03-15 07:29:38,271] [INFO] Target genome list was writen to OceanDNA-a1050/target_genomes_gtdb.txt
[2023-03-15 07:29:38,275] [INFO] Task started: fastANI
[2023-03-15 07:29:38,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg87865cdf-d43e-4179-88c3-47b7ed59f56d/OceanDNA-a1050.fa --refList OceanDNA-a1050/target_genomes_gtdb.txt --output OceanDNA-a1050/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:29:39,433] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:39,437] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:29:39,437] [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_018697035.1	s__JAGVXH01 sp018697035	99.9865	176	177	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018303845.1	s__JAGVXH01 sp018303845	79.0492	84	177	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018693315.1	s__JAGVXH01 sp018693315	78.3693	70	177	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:29:39,437] [INFO] GTDB search result was written to OceanDNA-a1050/result_gtdb.tsv
[2023-03-15 07:29:39,437] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:29:39,438] [INFO] DFAST_QC result json was written to OceanDNA-a1050/dqc_result.json
[2023-03-15 07:29:39,438] [INFO] DFAST_QC completed!
[2023-03-15 07:29:39,438] [INFO] Total running time: 0h0m28s