[2023-03-18 00:21:56,071] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:56,071] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:56,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference
[2023-03-18 00:21:57,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:57,143] [INFO] Task started: Prodigal
[2023-03-18 00:21:57,144] [INFO] Running command: cat /var/lib/cwl/stg0d291a26-457f-4dc2-ad4d-2c5227cf76ea/OceanDNA-b3657.fa | prodigal -d OceanDNA-b3657/cds.fna -a OceanDNA-b3657/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:07,969] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:07,969] [INFO] Task started: HMMsearch
[2023-03-18 00:22:07,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b3657/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/reference_markers.hmm OceanDNA-b3657/protein.faa > /dev/null
[2023-03-18 00:22:08,169] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:08,169] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0d291a26-457f-4dc2-ad4d-2c5227cf76ea/OceanDNA-b3657.fa]
[2023-03-18 00:22:08,185] [INFO] Query marker FASTA was written to OceanDNA-b3657/markers.fasta
[2023-03-18 00:22:08,186] [INFO] Task started: Blastn
[2023-03-18 00:22:08,186] [INFO] Running command: blastn -query OceanDNA-b3657/markers.fasta -db /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/reference_markers.fasta -out OceanDNA-b3657/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:08,740] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:08,741] [INFO] Selected 20 target genomes.
[2023-03-18 00:22:08,741] [INFO] Target genome list was writen to OceanDNA-b3657/target_genomes.txt
[2023-03-18 00:22:08,754] [INFO] Task started: fastANI
[2023-03-18 00:22:08,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d291a26-457f-4dc2-ad4d-2c5227cf76ea/OceanDNA-b3657.fa --refList OceanDNA-b3657/target_genomes.txt --output OceanDNA-b3657/fastani_result.tsv --threads 1
[2023-03-18 00:22:20,157] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:20,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:20,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:20,158] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:20,158] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:20,158] [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
--------------------------------------------------------------------------------
[2023-03-18 00:22:20,158] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3657/tc_result.tsv
[2023-03-18 00:22:20,158] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:20,159] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:20,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/checkm_data
[2023-03-18 00:22:20,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:20,165] [INFO] Task started: CheckM
[2023-03-18 00:22:20,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3657/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3657/checkm_input OceanDNA-b3657/checkm_result
[2023-03-18 00:22:51,468] [INFO] Task succeeded: CheckM
[2023-03-18 00:22:51,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.44%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:22:51,471] [INFO] ===== Completeness check finished =====
[2023-03-18 00:22:51,471] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:22:51,472] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3657/markers.fasta)
[2023-03-18 00:22:51,473] [INFO] Task started: Blastn
[2023-03-18 00:22:51,473] [INFO] Running command: blastn -query OceanDNA-b3657/markers.fasta -db /var/lib/cwl/stg4a1e8cd5-f1ae-47c0-8288-06e139e8823e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3657/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:52,440] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:52,441] [INFO] Selected 28 target genomes.
[2023-03-18 00:22:52,441] [INFO] Target genome list was writen to OceanDNA-b3657/target_genomes_gtdb.txt
[2023-03-18 00:22:52,548] [INFO] Task started: fastANI
[2023-03-18 00:22:52,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d291a26-457f-4dc2-ad4d-2c5227cf76ea/OceanDNA-b3657.fa --refList OceanDNA-b3657/target_genomes_gtdb.txt --output OceanDNA-b3657/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:07,577] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:07,577] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:07,577] [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
--------------------------------------------------------------------------------
[2023-03-18 00:23:07,578] [INFO] GTDB search result was written to OceanDNA-b3657/result_gtdb.tsv
[2023-03-18 00:23:07,578] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:07,578] [INFO] DFAST_QC result json was written to OceanDNA-b3657/dqc_result.json
[2023-03-18 00:23:07,578] [INFO] DFAST_QC completed!
[2023-03-18 00:23:07,578] [INFO] Total running time: 0h1m12s