[2023-03-14 11:36:02,656] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,656] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,407] [INFO] Running command: cat /var/lib/cwl/stgd9562d87-237d-4f1b-8803-e20a5a81914f/OceanDNA-b22999.fa | prodigal -d OceanDNA-b22999/cds.fna -a OceanDNA-b22999/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:11,617] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:11,617] [INFO] Task started: HMMsearch
[2023-03-14 11:36:11,617] [INFO] Running command: hmmsearch --tblout OceanDNA-b22999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/reference_markers.hmm OceanDNA-b22999/protein.faa > /dev/null
[2023-03-14 11:36:11,771] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:11,772] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9562d87-237d-4f1b-8803-e20a5a81914f/OceanDNA-b22999.fa]
[2023-03-14 11:36:11,786] [INFO] Query marker FASTA was written to OceanDNA-b22999/markers.fasta
[2023-03-14 11:36:11,788] [INFO] Task started: Blastn
[2023-03-14 11:36:11,788] [INFO] Running command: blastn -query OceanDNA-b22999/markers.fasta -db /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/reference_markers.fasta -out OceanDNA-b22999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:12,309] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:12,309] [INFO] Selected 21 target genomes.
[2023-03-14 11:36:12,310] [INFO] Target genome list was writen to OceanDNA-b22999/target_genomes.txt
[2023-03-14 11:36:12,320] [INFO] Task started: fastANI
[2023-03-14 11:36:12,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9562d87-237d-4f1b-8803-e20a5a81914f/OceanDNA-b22999.fa --refList OceanDNA-b22999/target_genomes.txt --output OceanDNA-b22999/fastani_result.tsv --threads 1
[2023-03-14 11:36:29,673] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:29,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:29,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:29,674] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:29,674] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:29,674] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:29,674] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22999/tc_result.tsv
[2023-03-14 11:36:29,674] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:29,675] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:29,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/checkm_data
[2023-03-14 11:36:29,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:29,681] [INFO] Task started: CheckM
[2023-03-14 11:36:29,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22999/checkm_input OceanDNA-b22999/checkm_result
[2023-03-14 11:36:54,320] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:54,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.27%
Contamintation: 5.59%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:54,323] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:54,323] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:54,323] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22999/markers.fasta)
[2023-03-14 11:36:54,324] [INFO] Task started: Blastn
[2023-03-14 11:36:54,324] [INFO] Running command: blastn -query OceanDNA-b22999/markers.fasta -db /var/lib/cwl/stgb91f954f-36b0-4ad2-aa9c-49381cc86928/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:55,067] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:55,068] [INFO] Selected 23 target genomes.
[2023-03-14 11:36:55,069] [INFO] Target genome list was writen to OceanDNA-b22999/target_genomes_gtdb.txt
[2023-03-14 11:36:55,127] [INFO] Task started: fastANI
[2023-03-14 11:36:55,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9562d87-237d-4f1b-8803-e20a5a81914f/OceanDNA-b22999.fa --refList OceanDNA-b22999/target_genomes_gtdb.txt --output OceanDNA-b22999/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:37:11,383] [INFO] Task succeeded: fastANI
[2023-03-14 11:37:11,386] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:37:11,386] [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_016709875.1	s__JADJLZ01 sp016709875	76.6973	50	271	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	76.6151	50	271	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_016714045.1	s__JADJNY01 sp016714045	76.4973	55	271	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:37:11,387] [INFO] GTDB search result was written to OceanDNA-b22999/result_gtdb.tsv
[2023-03-14 11:37:11,388] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:37:11,388] [INFO] DFAST_QC result json was written to OceanDNA-b22999/dqc_result.json
[2023-03-14 11:37:11,389] [INFO] DFAST_QC completed!
[2023-03-14 11:37:11,389] [INFO] Total running time: 0h1m9s