[2023-03-14 12:19:39,591] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,591] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference
[2023-03-14 12:19:40,704] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,704] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,704] [INFO] Running command: cat /var/lib/cwl/stg88468313-478f-4dd2-83a7-516158117138/OceanDNA-b332.fa | prodigal -d OceanDNA-b332/cds.fna -a OceanDNA-b332/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:19:46,697] [INFO] Task succeeded: Prodigal
[2023-03-14 12:19:46,698] [INFO] Task started: HMMsearch
[2023-03-14 12:19:46,698] [INFO] Running command: hmmsearch --tblout OceanDNA-b332/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/reference_markers.hmm OceanDNA-b332/protein.faa > /dev/null
[2023-03-14 12:19:46,834] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:19:46,834] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88468313-478f-4dd2-83a7-516158117138/OceanDNA-b332.fa]
[2023-03-14 12:19:46,852] [INFO] Query marker FASTA was written to OceanDNA-b332/markers.fasta
[2023-03-14 12:19:46,852] [INFO] Task started: Blastn
[2023-03-14 12:19:46,852] [INFO] Running command: blastn -query OceanDNA-b332/markers.fasta -db /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/reference_markers.fasta -out OceanDNA-b332/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:19:47,288] [INFO] Task succeeded: Blastn
[2023-03-14 12:19:47,290] [INFO] Selected 6 target genomes.
[2023-03-14 12:19:47,290] [INFO] Target genome list was writen to OceanDNA-b332/target_genomes.txt
[2023-03-14 12:19:47,294] [INFO] Task started: fastANI
[2023-03-14 12:19:47,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg88468313-478f-4dd2-83a7-516158117138/OceanDNA-b332.fa --refList OceanDNA-b332/target_genomes.txt --output OceanDNA-b332/fastani_result.tsv --threads 1
[2023-03-14 12:19:51,334] [INFO] Task succeeded: fastANI
[2023-03-14 12:19:51,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:19:51,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:19:51,335] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:19:51,335] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:19:51,335] [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 12:19:51,336] [INFO] DFAST Taxonomy check result was written to OceanDNA-b332/tc_result.tsv
[2023-03-14 12:19:51,337] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:19:51,337] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:19:51,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/checkm_data
[2023-03-14 12:19:51,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:19:51,344] [INFO] Task started: CheckM
[2023-03-14 12:19:51,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b332/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b332/checkm_input OceanDNA-b332/checkm_result
[2023-03-14 12:20:13,009] [INFO] Task succeeded: CheckM
[2023-03-14 12:20:13,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:20:13,036] [INFO] ===== Completeness check finished =====
[2023-03-14 12:20:13,036] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:20:13,036] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b332/markers.fasta)
[2023-03-14 12:20:13,036] [INFO] Task started: Blastn
[2023-03-14 12:20:13,036] [INFO] Running command: blastn -query OceanDNA-b332/markers.fasta -db /var/lib/cwl/stg5fe8d333-8f82-4517-a869-30f08cc78a99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b332/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:13,501] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:13,508] [INFO] Selected 9 target genomes.
[2023-03-14 12:20:13,508] [INFO] Target genome list was writen to OceanDNA-b332/target_genomes_gtdb.txt
[2023-03-14 12:20:13,540] [INFO] Task started: fastANI
[2023-03-14 12:20:13,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg88468313-478f-4dd2-83a7-516158117138/OceanDNA-b332.fa --refList OceanDNA-b332/target_genomes_gtdb.txt --output OceanDNA-b332/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:20:16,218] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:16,221] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:20:16,221] [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_009711295.1	s__F1-20-MAGs119 sp009711295	87.3616	155	178	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	98.43	97.32	0.85	0.80	3	-
GCA_903858075.1	s__F1-20-MAGs119 sp903858075	84.5475	126	178	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205145.1	s__F1-20-MAGs119 sp013205145	84.4138	136	178	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	96.62	96.62	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:20:16,226] [INFO] GTDB search result was written to OceanDNA-b332/result_gtdb.tsv
[2023-03-14 12:20:16,234] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:20:16,237] [INFO] DFAST_QC result json was written to OceanDNA-b332/dqc_result.json
[2023-03-14 12:20:16,237] [INFO] DFAST_QC completed!
[2023-03-14 12:20:16,237] [INFO] Total running time: 0h0m37s