[2023-03-19 04:29:37,740] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference
[2023-03-19 04:29:38,873] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,874] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,874] [INFO] Running command: cat /var/lib/cwl/stg68c45f5f-1258-4968-9354-92f2608fbbd5/OceanDNA-b15177.fa | prodigal -d OceanDNA-b15177/cds.fna -a OceanDNA-b15177/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:43,548] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:43,548] [INFO] Task started: HMMsearch
[2023-03-19 04:29:43,548] [INFO] Running command: hmmsearch --tblout OceanDNA-b15177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/reference_markers.hmm OceanDNA-b15177/protein.faa > /dev/null
[2023-03-19 04:29:43,698] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:43,699] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68c45f5f-1258-4968-9354-92f2608fbbd5/OceanDNA-b15177.fa]
[2023-03-19 04:29:43,706] [INFO] Query marker FASTA was written to OceanDNA-b15177/markers.fasta
[2023-03-19 04:29:43,706] [INFO] Task started: Blastn
[2023-03-19 04:29:43,706] [INFO] Running command: blastn -query OceanDNA-b15177/markers.fasta -db /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/reference_markers.fasta -out OceanDNA-b15177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:44,187] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:44,188] [INFO] Selected 10 target genomes.
[2023-03-19 04:29:44,188] [INFO] Target genome list was writen to OceanDNA-b15177/target_genomes.txt
[2023-03-19 04:29:44,193] [INFO] Task started: fastANI
[2023-03-19 04:29:44,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c45f5f-1258-4968-9354-92f2608fbbd5/OceanDNA-b15177.fa --refList OceanDNA-b15177/target_genomes.txt --output OceanDNA-b15177/fastani_result.tsv --threads 1
[2023-03-19 04:29:46,787] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:46,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:46,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:46,787] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:46,787] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:46,787] [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 04:29:46,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15177/tc_result.tsv
[2023-03-19 04:29:46,788] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:46,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:46,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/checkm_data
[2023-03-19 04:29:46,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:46,792] [INFO] Task started: CheckM
[2023-03-19 04:29:46,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15177/checkm_input OceanDNA-b15177/checkm_result
[2023-03-19 04:30:04,338] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:04,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:04,340] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:04,340] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:04,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15177/markers.fasta)
[2023-03-19 04:30:04,340] [INFO] Task started: Blastn
[2023-03-19 04:30:04,340] [INFO] Running command: blastn -query OceanDNA-b15177/markers.fasta -db /var/lib/cwl/stg1a17042e-d9ee-4634-a7e7-2635523b4fbd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:04,981] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:04,982] [INFO] Selected 19 target genomes.
[2023-03-19 04:30:04,982] [INFO] Target genome list was writen to OceanDNA-b15177/target_genomes_gtdb.txt
[2023-03-19 04:30:05,014] [INFO] Task started: fastANI
[2023-03-19 04:30:05,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c45f5f-1258-4968-9354-92f2608fbbd5/OceanDNA-b15177.fa --refList OceanDNA-b15177/target_genomes_gtdb.txt --output OceanDNA-b15177/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:10,764] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:10,767] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:10,767] [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_002710905.1	s__GCA-002718395 sp002710905	93.7374	209	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718395.1	s__GCA-002718395 sp002718395	84.851	93	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:10,767] [INFO] GTDB search result was written to OceanDNA-b15177/result_gtdb.tsv
[2023-03-19 04:30:10,767] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:10,768] [INFO] DFAST_QC result json was written to OceanDNA-b15177/dqc_result.json
[2023-03-19 04:30:10,768] [INFO] DFAST_QC completed!
[2023-03-19 04:30:10,768] [INFO] Total running time: 0h0m33s