[2023-03-17 00:36:57,826] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:36:57,826] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:36:57,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference
[2023-03-17 00:36:59,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:36:59,972] [INFO] Task started: Prodigal
[2023-03-17 00:36:59,972] [INFO] Running command: cat /var/lib/cwl/stgd0ec4e00-1b4e-4faa-af69-bd8b99649ac1/OceanDNA-b45302.fa | prodigal -d OceanDNA-b45302/cds.fna -a OceanDNA-b45302/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:37:11,082] [INFO] Task succeeded: Prodigal
[2023-03-17 00:37:11,082] [INFO] Task started: HMMsearch
[2023-03-17 00:37:11,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b45302/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/reference_markers.hmm OceanDNA-b45302/protein.faa > /dev/null
[2023-03-17 00:37:11,289] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:37:11,289] [INFO] Found 6/6 markers.
[2023-03-17 00:37:11,313] [INFO] Query marker FASTA was written to OceanDNA-b45302/markers.fasta
[2023-03-17 00:37:11,314] [INFO] Task started: Blastn
[2023-03-17 00:37:11,314] [INFO] Running command: blastn -query OceanDNA-b45302/markers.fasta -db /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/reference_markers.fasta -out OceanDNA-b45302/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:37:11,831] [INFO] Task succeeded: Blastn
[2023-03-17 00:37:11,832] [INFO] Selected 21 target genomes.
[2023-03-17 00:37:11,832] [INFO] Target genome list was writen to OceanDNA-b45302/target_genomes.txt
[2023-03-17 00:37:11,844] [INFO] Task started: fastANI
[2023-03-17 00:37:11,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ec4e00-1b4e-4faa-af69-bd8b99649ac1/OceanDNA-b45302.fa --refList OceanDNA-b45302/target_genomes.txt --output OceanDNA-b45302/fastani_result.tsv --threads 1
[2023-03-17 00:37:19,672] [INFO] Task succeeded: fastANI
[2023-03-17 00:37:19,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:37:19,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:37:19,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:37:19,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:37:19,673] [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
--------------------------------------------------------------------------------
[2023-03-17 00:37:19,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45302/tc_result.tsv
[2023-03-17 00:37:19,674] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:37:19,674] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:37:19,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/checkm_data
[2023-03-17 00:37:19,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:37:19,683] [INFO] Task started: CheckM
[2023-03-17 00:37:19,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45302/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45302/checkm_input OceanDNA-b45302/checkm_result
[2023-03-17 00:37:52,547] [INFO] Task succeeded: CheckM
[2023-03-17 00:37:52,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:37:52,550] [INFO] ===== Completeness check finished =====
[2023-03-17 00:37:52,550] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:37:52,550] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45302/markers.fasta)
[2023-03-17 00:37:52,551] [INFO] Task started: Blastn
[2023-03-17 00:37:52,552] [INFO] Running command: blastn -query OceanDNA-b45302/markers.fasta -db /var/lib/cwl/stgebe0996c-1cc5-4488-aef8-8d9596920d1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45302/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:37:53,272] [INFO] Task succeeded: Blastn
[2023-03-17 00:37:53,273] [INFO] Selected 30 target genomes.
[2023-03-17 00:37:53,273] [INFO] Target genome list was writen to OceanDNA-b45302/target_genomes_gtdb.txt
[2023-03-17 00:37:53,861] [INFO] Task started: fastANI
[2023-03-17 00:37:53,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ec4e00-1b4e-4faa-af69-bd8b99649ac1/OceanDNA-b45302.fa --refList OceanDNA-b45302/target_genomes_gtdb.txt --output OceanDNA-b45302/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:38:06,456] [INFO] Task succeeded: fastANI
[2023-03-17 00:38:06,458] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:38:06,459] [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_002402105.1	s__GCA-2402105 sp002402105	77.7198	151	536	d__Bacteria;p__UBP17;c__UBA6191;o__UBA6191;f__UBA6191;g__GCA-2402105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:38:06,459] [INFO] GTDB search result was written to OceanDNA-b45302/result_gtdb.tsv
[2023-03-17 00:38:06,459] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:38:06,459] [INFO] DFAST_QC result json was written to OceanDNA-b45302/dqc_result.json
[2023-03-17 00:38:06,459] [INFO] DFAST_QC completed!
[2023-03-17 00:38:06,459] [INFO] Total running time: 0h1m9s