[2023-03-19 01:33:27,234] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference
[2023-03-19 01:33:28,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,343] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,343] [INFO] Running command: cat /var/lib/cwl/stge9f03079-4685-4ea5-a2a4-95406484f017/OceanDNA-b30522.fa | prodigal -d OceanDNA-b30522/cds.fna -a OceanDNA-b30522/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:46,759] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:46,759] [INFO] Task started: HMMsearch
[2023-03-19 01:33:46,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b30522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/reference_markers.hmm OceanDNA-b30522/protein.faa > /dev/null
[2023-03-19 01:33:46,976] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:46,977] [INFO] Found 6/6 markers.
[2023-03-19 01:33:46,997] [INFO] Query marker FASTA was written to OceanDNA-b30522/markers.fasta
[2023-03-19 01:33:46,998] [INFO] Task started: Blastn
[2023-03-19 01:33:46,998] [INFO] Running command: blastn -query OceanDNA-b30522/markers.fasta -db /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/reference_markers.fasta -out OceanDNA-b30522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:47,576] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:47,577] [INFO] Selected 23 target genomes.
[2023-03-19 01:33:47,577] [INFO] Target genome list was writen to OceanDNA-b30522/target_genomes.txt
[2023-03-19 01:33:47,591] [INFO] Task started: fastANI
[2023-03-19 01:33:47,592] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f03079-4685-4ea5-a2a4-95406484f017/OceanDNA-b30522.fa --refList OceanDNA-b30522/target_genomes.txt --output OceanDNA-b30522/fastani_result.tsv --threads 1
[2023-03-19 01:33:59,289] [INFO] Task succeeded: fastANI
[2023-03-19 01:33:59,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:33:59,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:33:59,289] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:33:59,289] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:33:59,290] [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 01:33:59,290] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30522/tc_result.tsv
[2023-03-19 01:33:59,290] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:33:59,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:33:59,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/checkm_data
[2023-03-19 01:33:59,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:33:59,302] [INFO] Task started: CheckM
[2023-03-19 01:33:59,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30522/checkm_input OceanDNA-b30522/checkm_result
[2023-03-19 01:34:48,248] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:48,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:48,251] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:48,251] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:48,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30522/markers.fasta)
[2023-03-19 01:34:48,253] [INFO] Task started: Blastn
[2023-03-19 01:34:48,253] [INFO] Running command: blastn -query OceanDNA-b30522/markers.fasta -db /var/lib/cwl/stg6e2f8639-d1e0-417d-98d1-5238851ffa07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:49,191] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:49,192] [INFO] Selected 24 target genomes.
[2023-03-19 01:34:49,192] [INFO] Target genome list was writen to OceanDNA-b30522/target_genomes_gtdb.txt
[2023-03-19 01:34:49,216] [INFO] Task started: fastANI
[2023-03-19 01:34:49,216] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f03079-4685-4ea5-a2a4-95406484f017/OceanDNA-b30522.fa --refList OceanDNA-b30522/target_genomes_gtdb.txt --output OceanDNA-b30522/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:35:01,498] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:01,502] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:35:01,502] [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_905480645.1	s__Tateyamaria sp003445215	99.8445	948	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	98.75	98.35	0.86	0.66	9	conclusive
GCF_900143535.1	s__Tateyamaria sp900143535	76.334	53	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668195.1	s__Tateyamaria sp018668195	76.0393	54	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:35:01,502] [INFO] GTDB search result was written to OceanDNA-b30522/result_gtdb.tsv
[2023-03-19 01:35:01,502] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:35:01,503] [INFO] DFAST_QC result json was written to OceanDNA-b30522/dqc_result.json
[2023-03-19 01:35:01,503] [INFO] DFAST_QC completed!
[2023-03-19 01:35:01,503] [INFO] Total running time: 0h1m34s