[2023-03-15 15:55:16,217] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference
[2023-03-15 15:55:17,910] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,911] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,911] [INFO] Running command: cat /var/lib/cwl/stg26c5c0be-8b9b-40c0-a470-2269c52b12ee/OceanDNA-b17169.fa | prodigal -d OceanDNA-b17169/cds.fna -a OceanDNA-b17169/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:20,961] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:20,962] [INFO] Task started: HMMsearch
[2023-03-15 15:55:20,962] [INFO] Running command: hmmsearch --tblout OceanDNA-b17169/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/reference_markers.hmm OceanDNA-b17169/protein.faa > /dev/null
[2023-03-15 15:55:21,099] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:21,100] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg26c5c0be-8b9b-40c0-a470-2269c52b12ee/OceanDNA-b17169.fa]
[2023-03-15 15:55:21,105] [INFO] Query marker FASTA was written to OceanDNA-b17169/markers.fasta
[2023-03-15 15:55:21,105] [INFO] Task started: Blastn
[2023-03-15 15:55:21,105] [INFO] Running command: blastn -query OceanDNA-b17169/markers.fasta -db /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/reference_markers.fasta -out OceanDNA-b17169/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:23,465] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:23,466] [INFO] Selected 9 target genomes.
[2023-03-15 15:55:23,466] [INFO] Target genome list was writen to OceanDNA-b17169/target_genomes.txt
[2023-03-15 15:55:23,476] [INFO] Task started: fastANI
[2023-03-15 15:55:23,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c5c0be-8b9b-40c0-a470-2269c52b12ee/OceanDNA-b17169.fa --refList OceanDNA-b17169/target_genomes.txt --output OceanDNA-b17169/fastani_result.tsv --threads 1
[2023-03-15 15:55:25,049] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:25,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:25,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:25,053] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:25,053] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:25,053] [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
Mycoplasma todarodis	strain=5H	GCA_004335995.1	1937191	1937191	type	True	84.7936	90	134	95	below_threshold
Mycoplasma marinum	strain=PE	GCA_004335975.1	1937190	1937190	type	True	81.1067	69	134	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:25,053] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17169/tc_result.tsv
[2023-03-15 15:55:25,054] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:25,054] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:25,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/checkm_data
[2023-03-15 15:55:25,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:25,056] [INFO] Task started: CheckM
[2023-03-15 15:55:25,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17169/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17169/checkm_input OceanDNA-b17169/checkm_result
[2023-03-15 15:55:41,120] [INFO] Task succeeded: CheckM
[2023-03-15 15:55:41,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:55:41,123] [INFO] ===== Completeness check finished =====
[2023-03-15 15:55:41,123] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:55:41,123] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17169/markers.fasta)
[2023-03-15 15:55:41,125] [INFO] Task started: Blastn
[2023-03-15 15:55:41,125] [INFO] Running command: blastn -query OceanDNA-b17169/markers.fasta -db /var/lib/cwl/stgc10d8367-a3ee-490a-a810-8544ebaf75d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17169/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:41,932] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:41,933] [INFO] Selected 8 target genomes.
[2023-03-15 15:55:41,933] [INFO] Target genome list was writen to OceanDNA-b17169/target_genomes_gtdb.txt
[2023-03-15 15:55:41,944] [INFO] Task started: fastANI
[2023-03-15 15:55:41,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c5c0be-8b9b-40c0-a470-2269c52b12ee/OceanDNA-b17169.fa --refList OceanDNA-b17169/target_genomes_gtdb.txt --output OceanDNA-b17169/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:55:43,343] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:43,347] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:55:43,347] [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_013215715.1	s__Mycoplasma_K sp013215715	99.9883	131	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004335995.1	s__Mycoplasma_K todarodis	84.9106	89	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335975.1	s__Mycoplasma_K marinum	81.1067	69	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:55:43,347] [INFO] GTDB search result was written to OceanDNA-b17169/result_gtdb.tsv
[2023-03-15 15:55:43,347] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:55:43,348] [INFO] DFAST_QC result json was written to OceanDNA-b17169/dqc_result.json
[2023-03-15 15:55:43,348] [INFO] DFAST_QC completed!
[2023-03-15 15:55:43,348] [INFO] Total running time: 0h0m27s