[2023-03-14 13:19:07,366] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:19:07,366] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:19:07,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference
[2023-03-14 13:19:08,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:19:08,535] [INFO] Task started: Prodigal
[2023-03-14 13:19:08,535] [INFO] Running command: cat /var/lib/cwl/stgb36ce52c-0c8a-44f1-b9ed-b428d0d89eaa/OceanDNA-b660.fa | prodigal -d OceanDNA-b660/cds.fna -a OceanDNA-b660/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:19:18,046] [INFO] Task succeeded: Prodigal
[2023-03-14 13:19:18,046] [INFO] Task started: HMMsearch
[2023-03-14 13:19:18,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/reference_markers.hmm OceanDNA-b660/protein.faa > /dev/null
[2023-03-14 13:19:18,298] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:19:18,299] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb36ce52c-0c8a-44f1-b9ed-b428d0d89eaa/OceanDNA-b660.fa]
[2023-03-14 13:19:18,313] [INFO] Query marker FASTA was written to OceanDNA-b660/markers.fasta
[2023-03-14 13:19:18,313] [INFO] Task started: Blastn
[2023-03-14 13:19:18,314] [INFO] Running command: blastn -query OceanDNA-b660/markers.fasta -db /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/reference_markers.fasta -out OceanDNA-b660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:19:18,833] [INFO] Task succeeded: Blastn
[2023-03-14 13:19:18,835] [INFO] Selected 15 target genomes.
[2023-03-14 13:19:18,835] [INFO] Target genome list was writen to OceanDNA-b660/target_genomes.txt
[2023-03-14 13:19:18,841] [INFO] Task started: fastANI
[2023-03-14 13:19:18,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36ce52c-0c8a-44f1-b9ed-b428d0d89eaa/OceanDNA-b660.fa --refList OceanDNA-b660/target_genomes.txt --output OceanDNA-b660/fastani_result.tsv --threads 1
[2023-03-14 13:19:29,571] [INFO] Task succeeded: fastANI
[2023-03-14 13:19:29,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:19:29,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:19:29,571] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:19:29,571] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:19:29,571] [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 13:19:29,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b660/tc_result.tsv
[2023-03-14 13:19:29,574] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:19:29,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:19:29,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/checkm_data
[2023-03-14 13:19:29,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:19:29,582] [INFO] Task started: CheckM
[2023-03-14 13:19:29,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b660/checkm_input OceanDNA-b660/checkm_result
[2023-03-14 13:19:53,927] [INFO] Task succeeded: CheckM
[2023-03-14 13:19:53,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:19:53,931] [INFO] ===== Completeness check finished =====
[2023-03-14 13:19:53,931] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:19:53,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b660/markers.fasta)
[2023-03-14 13:19:53,932] [INFO] Task started: Blastn
[2023-03-14 13:19:53,932] [INFO] Running command: blastn -query OceanDNA-b660/markers.fasta -db /var/lib/cwl/stgbfb04244-40c4-4894-9407-605b1ecdf00b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:19:54,568] [INFO] Task succeeded: Blastn
[2023-03-14 13:19:54,569] [INFO] Selected 28 target genomes.
[2023-03-14 13:19:54,569] [INFO] Target genome list was writen to OceanDNA-b660/target_genomes_gtdb.txt
[2023-03-14 13:19:54,646] [INFO] Task started: fastANI
[2023-03-14 13:19:54,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36ce52c-0c8a-44f1-b9ed-b428d0d89eaa/OceanDNA-b660.fa --refList OceanDNA-b660/target_genomes_gtdb.txt --output OceanDNA-b660/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:20:04,926] [INFO] Task succeeded: fastANI
[2023-03-14 13:20:04,928] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:20:04,928] [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_002729765.1	s__MedAcidi-G1 sp002729765	76.3468	58	395	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	98.94	98.94	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:20:04,929] [INFO] GTDB search result was written to OceanDNA-b660/result_gtdb.tsv
[2023-03-14 13:20:04,929] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:20:04,931] [INFO] DFAST_QC result json was written to OceanDNA-b660/dqc_result.json
[2023-03-14 13:20:04,931] [INFO] DFAST_QC completed!
[2023-03-14 13:20:04,931] [INFO] Total running time: 0h0m58s