[2023-03-15 05:36:19,903] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:36:19,904] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:36:19,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference
[2023-03-15 05:36:21,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:36:21,005] [INFO] Task started: Prodigal
[2023-03-15 05:36:21,005] [INFO] Running command: cat /var/lib/cwl/stg8e4c41b0-44af-4d5d-b211-8818ca675648/OceanDNA-b22181.fa | prodigal -d OceanDNA-b22181/cds.fna -a OceanDNA-b22181/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:36:26,799] [INFO] Task succeeded: Prodigal
[2023-03-15 05:36:26,799] [INFO] Task started: HMMsearch
[2023-03-15 05:36:26,799] [INFO] Running command: hmmsearch --tblout OceanDNA-b22181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/reference_markers.hmm OceanDNA-b22181/protein.faa > /dev/null
[2023-03-15 05:36:26,956] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:36:26,957] [INFO] Found 6/6 markers.
[2023-03-15 05:36:26,969] [INFO] Query marker FASTA was written to OceanDNA-b22181/markers.fasta
[2023-03-15 05:36:26,971] [INFO] Task started: Blastn
[2023-03-15 05:36:26,971] [INFO] Running command: blastn -query OceanDNA-b22181/markers.fasta -db /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/reference_markers.fasta -out OceanDNA-b22181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:36:27,530] [INFO] Task succeeded: Blastn
[2023-03-15 05:36:27,530] [INFO] Selected 11 target genomes.
[2023-03-15 05:36:27,531] [INFO] Target genome list was writen to OceanDNA-b22181/target_genomes.txt
[2023-03-15 05:36:27,541] [INFO] Task started: fastANI
[2023-03-15 05:36:27,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4c41b0-44af-4d5d-b211-8818ca675648/OceanDNA-b22181.fa --refList OceanDNA-b22181/target_genomes.txt --output OceanDNA-b22181/fastani_result.tsv --threads 1
[2023-03-15 05:36:33,836] [INFO] Task succeeded: fastANI
[2023-03-15 05:36:33,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:36:33,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:36:33,837] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:36:33,837] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:36:33,837] [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 05:36:33,837] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22181/tc_result.tsv
[2023-03-15 05:36:33,837] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:36:33,837] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:36:33,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/checkm_data
[2023-03-15 05:36:33,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:36:34,548] [INFO] Task started: CheckM
[2023-03-15 05:36:34,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22181/checkm_input OceanDNA-b22181/checkm_result
[2023-03-15 05:36:56,075] [INFO] Task succeeded: CheckM
[2023-03-15 05:36:56,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.35%
Contamintation: 1.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:36:56,077] [INFO] ===== Completeness check finished =====
[2023-03-15 05:36:56,077] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:36:56,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22181/markers.fasta)
[2023-03-15 05:36:56,079] [INFO] Task started: Blastn
[2023-03-15 05:36:56,079] [INFO] Running command: blastn -query OceanDNA-b22181/markers.fasta -db /var/lib/cwl/stg7b64d1e0-9ddf-4478-94d7-5d0f13ec30ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:36:57,003] [INFO] Task succeeded: Blastn
[2023-03-15 05:36:57,004] [INFO] Selected 18 target genomes.
[2023-03-15 05:36:57,004] [INFO] Target genome list was writen to OceanDNA-b22181/target_genomes_gtdb.txt
[2023-03-15 05:36:57,011] [INFO] Task started: fastANI
[2023-03-15 05:36:57,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4c41b0-44af-4d5d-b211-8818ca675648/OceanDNA-b22181.fa --refList OceanDNA-b22181/target_genomes_gtdb.txt --output OceanDNA-b22181/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:37:04,122] [INFO] Task succeeded: fastANI
[2023-03-15 05:37:04,125] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:37:04,125] [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_002718515.1	s__GCA-002718515 sp002718515	98.5228	207	230	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016845245.1	s__GCA-002718515 sp016845245	79.6055	133	230	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:37:04,125] [INFO] GTDB search result was written to OceanDNA-b22181/result_gtdb.tsv
[2023-03-15 05:37:04,125] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:37:04,125] [INFO] DFAST_QC result json was written to OceanDNA-b22181/dqc_result.json
[2023-03-15 05:37:04,126] [INFO] DFAST_QC completed!
[2023-03-15 05:37:04,126] [INFO] Total running time: 0h0m44s