[2023-03-16 07:28:30,040] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,040] [INFO] DQC Reference Directory: /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference
[2023-03-16 07:28:31,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,171] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,171] [INFO] Running command: cat /var/lib/cwl/stg19e3815c-1559-4fa0-b083-f81db47f283b/OceanDNA-a5189.fa | prodigal -d OceanDNA-a5189/cds.fna -a OceanDNA-a5189/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:41,480] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:41,480] [INFO] Task started: HMMsearch
[2023-03-16 07:28:41,480] [INFO] Running command: hmmsearch --tblout OceanDNA-a5189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/reference_markers.hmm OceanDNA-a5189/protein.faa > /dev/null
[2023-03-16 07:28:41,619] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:41,620] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg19e3815c-1559-4fa0-b083-f81db47f283b/OceanDNA-a5189.fa]
[2023-03-16 07:28:41,634] [INFO] Query marker FASTA was written to OceanDNA-a5189/markers.fasta
[2023-03-16 07:28:41,634] [INFO] Task started: Blastn
[2023-03-16 07:28:41,635] [INFO] Running command: blastn -query OceanDNA-a5189/markers.fasta -db /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/reference_markers.fasta -out OceanDNA-a5189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:42,084] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:42,086] [INFO] Selected 1 target genomes.
[2023-03-16 07:28:42,086] [INFO] Target genome list was writen to OceanDNA-a5189/target_genomes.txt
[2023-03-16 07:28:42,087] [INFO] Task started: fastANI
[2023-03-16 07:28:42,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e3815c-1559-4fa0-b083-f81db47f283b/OceanDNA-a5189.fa --refList OceanDNA-a5189/target_genomes.txt --output OceanDNA-a5189/fastani_result.tsv --threads 1
[2023-03-16 07:28:42,560] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:42,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:42,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:42,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:42,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:42,560] [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 07:28:42,562] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5189/tc_result.tsv
[2023-03-16 07:28:42,562] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:42,562] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:42,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/checkm_data
[2023-03-16 07:28:42,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:42,574] [INFO] Task started: CheckM
[2023-03-16 07:28:42,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5189/checkm_input OceanDNA-a5189/checkm_result
[2023-03-16 07:29:13,412] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:13,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:13,415] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:13,415] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:13,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5189/markers.fasta)
[2023-03-16 07:29:13,422] [INFO] Task started: Blastn
[2023-03-16 07:29:13,422] [INFO] Running command: blastn -query OceanDNA-a5189/markers.fasta -db /var/lib/cwl/stge4859fbd-4648-406a-839e-c48bcb6bcbed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:13,851] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:13,853] [INFO] Selected 8 target genomes.
[2023-03-16 07:29:13,853] [INFO] Target genome list was writen to OceanDNA-a5189/target_genomes_gtdb.txt
[2023-03-16 07:29:14,056] [INFO] Task started: fastANI
[2023-03-16 07:29:14,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e3815c-1559-4fa0-b083-f81db47f283b/OceanDNA-a5189.fa --refList OceanDNA-a5189/target_genomes_gtdb.txt --output OceanDNA-a5189/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:16,370] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:16,372] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:16,372] [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_002505495.1	s__MGIIb-Q1 sp002505495	80.9301	359	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:16,373] [INFO] GTDB search result was written to OceanDNA-a5189/result_gtdb.tsv
[2023-03-16 07:29:16,374] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:16,375] [INFO] DFAST_QC result json was written to OceanDNA-a5189/dqc_result.json
[2023-03-16 07:29:16,375] [INFO] DFAST_QC completed!
[2023-03-16 07:29:16,375] [INFO] Total running time: 0h0m46s