[2023-03-16 04:20:43,528] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference
[2023-03-16 04:20:44,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,640] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,641] [INFO] Running command: cat /var/lib/cwl/stg46bfee1e-ae58-4e08-a9c7-09779da3461a/OceanDNA-b16048.fa | prodigal -d OceanDNA-b16048/cds.fna -a OceanDNA-b16048/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:56,674] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:56,675] [INFO] Task started: HMMsearch
[2023-03-16 04:20:56,675] [INFO] Running command: hmmsearch --tblout OceanDNA-b16048/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/reference_markers.hmm OceanDNA-b16048/protein.faa > /dev/null
[2023-03-16 04:20:56,876] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:56,877] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg46bfee1e-ae58-4e08-a9c7-09779da3461a/OceanDNA-b16048.fa]
[2023-03-16 04:20:56,898] [INFO] Query marker FASTA was written to OceanDNA-b16048/markers.fasta
[2023-03-16 04:20:56,898] [INFO] Task started: Blastn
[2023-03-16 04:20:56,898] [INFO] Running command: blastn -query OceanDNA-b16048/markers.fasta -db /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/reference_markers.fasta -out OceanDNA-b16048/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:57,433] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:57,434] [INFO] Selected 20 target genomes.
[2023-03-16 04:20:57,434] [INFO] Target genome list was writen to OceanDNA-b16048/target_genomes.txt
[2023-03-16 04:20:57,447] [INFO] Task started: fastANI
[2023-03-16 04:20:57,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg46bfee1e-ae58-4e08-a9c7-09779da3461a/OceanDNA-b16048.fa --refList OceanDNA-b16048/target_genomes.txt --output OceanDNA-b16048/fastani_result.tsv --threads 1
[2023-03-16 04:21:10,382] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:10,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:21:10,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:21:10,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:21:10,383] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:21:10,383] [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
--------------------------------------------------------------------------------
[2023-03-16 04:21:10,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16048/tc_result.tsv
[2023-03-16 04:21:10,383] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:21:10,383] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:21:10,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/checkm_data
[2023-03-16 04:21:10,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:21:10,390] [INFO] Task started: CheckM
[2023-03-16 04:21:10,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16048/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16048/checkm_input OceanDNA-b16048/checkm_result
[2023-03-16 04:21:44,471] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:44,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.65%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:44,474] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:44,474] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:44,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16048/markers.fasta)
[2023-03-16 04:21:44,475] [INFO] Task started: Blastn
[2023-03-16 04:21:44,475] [INFO] Running command: blastn -query OceanDNA-b16048/markers.fasta -db /var/lib/cwl/stg92d7d488-e8e0-46a4-8ac1-bc0dffc12ad0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16048/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:45,307] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:45,308] [INFO] Selected 16 target genomes.
[2023-03-16 04:21:45,308] [INFO] Target genome list was writen to OceanDNA-b16048/target_genomes_gtdb.txt
[2023-03-16 04:21:45,327] [INFO] Task started: fastANI
[2023-03-16 04:21:45,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg46bfee1e-ae58-4e08-a9c7-09779da3461a/OceanDNA-b16048.fa --refList OceanDNA-b16048/target_genomes_gtdb.txt --output OceanDNA-b16048/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:21:57,252] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:57,256] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:21:57,256] [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
GCF_001904615.1	s__Limnothrix rosea	82.8498	566	698	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316605.1	s__Limnothrix sp000316605	79.5071	455	698	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033055.1	s__Limnothrix sp012033055	77.4479	261	698	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693255.1	s__Limnothrix sp001693255	76.2985	140	698	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:21:57,256] [INFO] GTDB search result was written to OceanDNA-b16048/result_gtdb.tsv
[2023-03-16 04:21:57,256] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:21:57,257] [INFO] DFAST_QC result json was written to OceanDNA-b16048/dqc_result.json
[2023-03-16 04:21:57,257] [INFO] DFAST_QC completed!
[2023-03-16 04:21:57,257] [INFO] Total running time: 0h1m14s