[2023-03-16 10:05:25,227] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:05:25,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:05:25,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference
[2023-03-16 10:05:26,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:05:26,451] [INFO] Task started: Prodigal
[2023-03-16 10:05:26,452] [INFO] Running command: cat /var/lib/cwl/stg35715c71-d5e1-45b9-9eec-0f33e94ca070/OceanDNA-b35948.fa | prodigal -d OceanDNA-b35948/cds.fna -a OceanDNA-b35948/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:05:34,907] [INFO] Task succeeded: Prodigal
[2023-03-16 10:05:34,907] [INFO] Task started: HMMsearch
[2023-03-16 10:05:34,907] [INFO] Running command: hmmsearch --tblout OceanDNA-b35948/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/reference_markers.hmm OceanDNA-b35948/protein.faa > /dev/null
[2023-03-16 10:05:35,082] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:05:35,082] [INFO] Found 6/6 markers.
[2023-03-16 10:05:35,095] [INFO] Query marker FASTA was written to OceanDNA-b35948/markers.fasta
[2023-03-16 10:05:35,096] [INFO] Task started: Blastn
[2023-03-16 10:05:35,096] [INFO] Running command: blastn -query OceanDNA-b35948/markers.fasta -db /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/reference_markers.fasta -out OceanDNA-b35948/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:05:35,817] [INFO] Task succeeded: Blastn
[2023-03-16 10:05:35,818] [INFO] Selected 33 target genomes.
[2023-03-16 10:05:35,818] [INFO] Target genome list was writen to OceanDNA-b35948/target_genomes.txt
[2023-03-16 10:05:35,839] [INFO] Task started: fastANI
[2023-03-16 10:05:35,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg35715c71-d5e1-45b9-9eec-0f33e94ca070/OceanDNA-b35948.fa --refList OceanDNA-b35948/target_genomes.txt --output OceanDNA-b35948/fastani_result.tsv --threads 1
[2023-03-16 10:05:52,437] [INFO] Task succeeded: fastANI
[2023-03-16 10:05:52,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:05:52,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:05:52,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:05:52,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:05:52,438] [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 10:05:52,438] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35948/tc_result.tsv
[2023-03-16 10:05:52,438] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:05:52,438] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:05:52,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/checkm_data
[2023-03-16 10:05:52,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:05:52,738] [INFO] Task started: CheckM
[2023-03-16 10:05:52,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35948/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35948/checkm_input OceanDNA-b35948/checkm_result
[2023-03-16 10:06:21,897] [INFO] Task succeeded: CheckM
[2023-03-16 10:06:21,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:06:21,904] [INFO] ===== Completeness check finished =====
[2023-03-16 10:06:21,904] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:06:21,904] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35948/markers.fasta)
[2023-03-16 10:06:21,905] [INFO] Task started: Blastn
[2023-03-16 10:06:21,905] [INFO] Running command: blastn -query OceanDNA-b35948/markers.fasta -db /var/lib/cwl/stg141d5546-0580-42a3-ad6c-a4232e095867/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35948/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:06:22,860] [INFO] Task succeeded: Blastn
[2023-03-16 10:06:22,861] [INFO] Selected 33 target genomes.
[2023-03-16 10:06:22,861] [INFO] Target genome list was writen to OceanDNA-b35948/target_genomes_gtdb.txt
[2023-03-16 10:06:22,894] [INFO] Task started: fastANI
[2023-03-16 10:06:22,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg35715c71-d5e1-45b9-9eec-0f33e94ca070/OceanDNA-b35948.fa --refList OceanDNA-b35948/target_genomes_gtdb.txt --output OceanDNA-b35948/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:06:39,357] [INFO] Task succeeded: fastANI
[2023-03-16 10:06:39,360] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:06:39,360] [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_009995425.1	s__JAALKW01 sp009995425	79.2305	226	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__JAALKW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087865.1	s__JAALKW01 sp011087865	76.7763	74	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__JAALKW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:06:39,360] [INFO] GTDB search result was written to OceanDNA-b35948/result_gtdb.tsv
[2023-03-16 10:06:39,360] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:06:39,361] [INFO] DFAST_QC result json was written to OceanDNA-b35948/dqc_result.json
[2023-03-16 10:06:39,361] [INFO] DFAST_QC completed!
[2023-03-16 10:06:39,361] [INFO] Total running time: 0h1m14s