[2023-03-15 15:18:22,041] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference
[2023-03-15 15:18:23,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,184] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,184] [INFO] Running command: cat /var/lib/cwl/stg5b36f787-ca68-4283-941f-c3bfc7ed450d/OceanDNA-b37974.fa | prodigal -d OceanDNA-b37974/cds.fna -a OceanDNA-b37974/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:41,262] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:41,262] [INFO] Task started: HMMsearch
[2023-03-15 15:18:41,262] [INFO] Running command: hmmsearch --tblout OceanDNA-b37974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/reference_markers.hmm OceanDNA-b37974/protein.faa > /dev/null
[2023-03-15 15:18:41,471] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:41,471] [INFO] Found 6/6 markers.
[2023-03-15 15:18:41,497] [INFO] Query marker FASTA was written to OceanDNA-b37974/markers.fasta
[2023-03-15 15:18:41,498] [INFO] Task started: Blastn
[2023-03-15 15:18:41,498] [INFO] Running command: blastn -query OceanDNA-b37974/markers.fasta -db /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/reference_markers.fasta -out OceanDNA-b37974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:42,070] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:42,074] [INFO] Selected 30 target genomes.
[2023-03-15 15:18:42,074] [INFO] Target genome list was writen to OceanDNA-b37974/target_genomes.txt
[2023-03-15 15:18:42,096] [INFO] Task started: fastANI
[2023-03-15 15:18:42,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b36f787-ca68-4283-941f-c3bfc7ed450d/OceanDNA-b37974.fa --refList OceanDNA-b37974/target_genomes.txt --output OceanDNA-b37974/fastani_result.tsv --threads 1
[2023-03-15 15:18:58,931] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:58,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:58,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:58,932] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:58,932] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:58,932] [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
--------------------------------------------------------------------------------
[2023-03-15 15:18:58,934] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37974/tc_result.tsv
[2023-03-15 15:18:58,937] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:58,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:58,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/checkm_data
[2023-03-15 15:18:58,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:58,946] [INFO] Task started: CheckM
[2023-03-15 15:18:58,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37974/checkm_input OceanDNA-b37974/checkm_result
[2023-03-15 15:19:45,121] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:45,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:45,145] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:45,146] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:45,146] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37974/markers.fasta)
[2023-03-15 15:19:45,147] [INFO] Task started: Blastn
[2023-03-15 15:19:45,147] [INFO] Running command: blastn -query OceanDNA-b37974/markers.fasta -db /var/lib/cwl/stgc8391285-977c-4c45-b07a-d4775953ec2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:46,081] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:46,083] [INFO] Selected 33 target genomes.
[2023-03-15 15:19:46,083] [INFO] Target genome list was writen to OceanDNA-b37974/target_genomes_gtdb.txt
[2023-03-15 15:19:46,106] [INFO] Task started: fastANI
[2023-03-15 15:19:46,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b36f787-ca68-4283-941f-c3bfc7ed450d/OceanDNA-b37974.fa --refList OceanDNA-b37974/target_genomes_gtdb.txt --output OceanDNA-b37974/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:20:03,044] [INFO] Task succeeded: fastANI
[2023-03-15 15:20:03,045] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:20:03,046] [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_905479205.1	s__Luminiphilus sp905479205	76.4506	67	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.27	99.27	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:20:03,048] [INFO] GTDB search result was written to OceanDNA-b37974/result_gtdb.tsv
[2023-03-15 15:20:03,048] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:20:03,051] [INFO] DFAST_QC result json was written to OceanDNA-b37974/dqc_result.json
[2023-03-15 15:20:03,051] [INFO] DFAST_QC completed!
[2023-03-15 15:20:03,051] [INFO] Total running time: 0h1m41s