[2023-03-18 02:53:05,583] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:53:05,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:53:05,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference
[2023-03-18 02:53:07,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:53:07,190] [INFO] Task started: Prodigal
[2023-03-18 02:53:07,190] [INFO] Running command: cat /var/lib/cwl/stg39caf8ff-53aa-4277-8a63-c7bb0e4279c2/OceanDNA-b17576.fa | prodigal -d OceanDNA-b17576/cds.fna -a OceanDNA-b17576/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:53:32,657] [INFO] Task succeeded: Prodigal
[2023-03-18 02:53:32,658] [INFO] Task started: HMMsearch
[2023-03-18 02:53:32,658] [INFO] Running command: hmmsearch --tblout OceanDNA-b17576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/reference_markers.hmm OceanDNA-b17576/protein.faa > /dev/null
[2023-03-18 02:53:32,888] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:53:32,889] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39caf8ff-53aa-4277-8a63-c7bb0e4279c2/OceanDNA-b17576.fa]
[2023-03-18 02:53:32,920] [INFO] Query marker FASTA was written to OceanDNA-b17576/markers.fasta
[2023-03-18 02:53:32,921] [INFO] Task started: Blastn
[2023-03-18 02:53:32,921] [INFO] Running command: blastn -query OceanDNA-b17576/markers.fasta -db /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/reference_markers.fasta -out OceanDNA-b17576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:53:33,458] [INFO] Task succeeded: Blastn
[2023-03-18 02:53:33,459] [INFO] Selected 12 target genomes.
[2023-03-18 02:53:33,460] [INFO] Target genome list was writen to OceanDNA-b17576/target_genomes.txt
[2023-03-18 02:53:33,466] [INFO] Task started: fastANI
[2023-03-18 02:53:33,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg39caf8ff-53aa-4277-8a63-c7bb0e4279c2/OceanDNA-b17576.fa --refList OceanDNA-b17576/target_genomes.txt --output OceanDNA-b17576/fastani_result.tsv --threads 1
[2023-03-18 02:53:38,294] [INFO] Task succeeded: fastANI
[2023-03-18 02:53:38,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:53:38,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:53:38,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:53:38,295] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:53:38,295] [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 02:53:38,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17576/tc_result.tsv
[2023-03-18 02:53:38,295] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:53:38,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:53:38,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/checkm_data
[2023-03-18 02:53:38,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:53:38,365] [INFO] Task started: CheckM
[2023-03-18 02:53:38,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17576/checkm_input OceanDNA-b17576/checkm_result
[2023-03-18 02:54:42,977] [INFO] Task succeeded: CheckM
[2023-03-18 02:54:42,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:54:42,981] [INFO] ===== Completeness check finished =====
[2023-03-18 02:54:42,982] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:54:42,982] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17576/markers.fasta)
[2023-03-18 02:54:42,982] [INFO] Task started: Blastn
[2023-03-18 02:54:42,982] [INFO] Running command: blastn -query OceanDNA-b17576/markers.fasta -db /var/lib/cwl/stg870130bc-3faf-4d2d-aad8-e9521fd4b988/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:54:43,774] [INFO] Task succeeded: Blastn
[2023-03-18 02:54:43,775] [INFO] Selected 22 target genomes.
[2023-03-18 02:54:43,775] [INFO] Target genome list was writen to OceanDNA-b17576/target_genomes_gtdb.txt
[2023-03-18 02:54:44,111] [INFO] Task started: fastANI
[2023-03-18 02:54:44,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg39caf8ff-53aa-4277-8a63-c7bb0e4279c2/OceanDNA-b17576.fa --refList OceanDNA-b17576/target_genomes_gtdb.txt --output OceanDNA-b17576/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:54:56,047] [INFO] Task succeeded: fastANI
[2023-03-18 02:54:56,049] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:54:56,049] [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_018650745.1	s__JABIFK01 sp018650745	79.6816	568	1312	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__JABIFK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:54:56,049] [INFO] GTDB search result was written to OceanDNA-b17576/result_gtdb.tsv
[2023-03-18 02:54:56,049] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:54:56,050] [INFO] DFAST_QC result json was written to OceanDNA-b17576/dqc_result.json
[2023-03-18 02:54:56,050] [INFO] DFAST_QC completed!
[2023-03-18 02:54:56,050] [INFO] Total running time: 0h1m50s