[2023-03-19 01:13:44,404] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,404] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference
[2023-03-19 01:13:45,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,517] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,517] [INFO] Running command: cat /var/lib/cwl/stgc782d5b6-c8d0-45f9-9453-58e9fb8801ca/OceanDNA-b30774.fa | prodigal -d OceanDNA-b30774/cds.fna -a OceanDNA-b30774/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:57,969] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:57,969] [INFO] Task started: HMMsearch
[2023-03-19 01:13:57,970] [INFO] Running command: hmmsearch --tblout OceanDNA-b30774/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/reference_markers.hmm OceanDNA-b30774/protein.faa > /dev/null
[2023-03-19 01:13:58,163] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:58,163] [INFO] Found 6/6 markers.
[2023-03-19 01:13:58,182] [INFO] Query marker FASTA was written to OceanDNA-b30774/markers.fasta
[2023-03-19 01:13:58,183] [INFO] Task started: Blastn
[2023-03-19 01:13:58,183] [INFO] Running command: blastn -query OceanDNA-b30774/markers.fasta -db /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/reference_markers.fasta -out OceanDNA-b30774/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:58,815] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:58,816] [INFO] Selected 35 target genomes.
[2023-03-19 01:13:58,817] [INFO] Target genome list was writen to OceanDNA-b30774/target_genomes.txt
[2023-03-19 01:13:58,837] [INFO] Task started: fastANI
[2023-03-19 01:13:58,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782d5b6-c8d0-45f9-9453-58e9fb8801ca/OceanDNA-b30774.fa --refList OceanDNA-b30774/target_genomes.txt --output OceanDNA-b30774/fastani_result.tsv --threads 1
[2023-03-19 01:14:23,799] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:23,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:23,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:23,799] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:23,799] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:23,800] [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 01:14:23,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30774/tc_result.tsv
[2023-03-19 01:14:23,800] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:23,800] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:23,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/checkm_data
[2023-03-19 01:14:23,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:23,869] [INFO] Task started: CheckM
[2023-03-19 01:14:23,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30774/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30774/checkm_input OceanDNA-b30774/checkm_result
[2023-03-19 01:15:00,192] [INFO] Task succeeded: CheckM
[2023-03-19 01:15:00,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.65%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:15:00,195] [INFO] ===== Completeness check finished =====
[2023-03-19 01:15:00,196] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:15:00,196] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30774/markers.fasta)
[2023-03-19 01:15:00,196] [INFO] Task started: Blastn
[2023-03-19 01:15:00,197] [INFO] Running command: blastn -query OceanDNA-b30774/markers.fasta -db /var/lib/cwl/stg5f757ed5-4034-4e5d-8ce0-4680e5fe8b73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30774/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:15:01,303] [INFO] Task succeeded: Blastn
[2023-03-19 01:15:01,304] [INFO] Selected 35 target genomes.
[2023-03-19 01:15:01,304] [INFO] Target genome list was writen to OceanDNA-b30774/target_genomes_gtdb.txt
[2023-03-19 01:15:01,331] [INFO] Task started: fastANI
[2023-03-19 01:15:01,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782d5b6-c8d0-45f9-9453-58e9fb8801ca/OceanDNA-b30774.fa --refList OceanDNA-b30774/target_genomes_gtdb.txt --output OceanDNA-b30774/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:15:21,469] [INFO] Task succeeded: fastANI
[2023-03-19 01:15:21,472] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:15:21,472] [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_018662225.1	s__JABJGO01 sp018662225	76.3271	68	589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JABJGO01	95.0	99.91	99.87	0.94	0.92	10	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	76.1848	60	589	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:15:21,472] [INFO] GTDB search result was written to OceanDNA-b30774/result_gtdb.tsv
[2023-03-19 01:15:21,472] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:15:21,473] [INFO] DFAST_QC result json was written to OceanDNA-b30774/dqc_result.json
[2023-03-19 01:15:21,473] [INFO] DFAST_QC completed!
[2023-03-19 01:15:21,473] [INFO] Total running time: 0h1m37s