[2023-03-16 08:50:59,647] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,647] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference
[2023-03-16 08:51:00,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,730] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,731] [INFO] Running command: cat /var/lib/cwl/stg2ceab5f4-3a87-4da3-898f-cc5a2e6753de/OceanDNA-b14012.fa | prodigal -d OceanDNA-b14012/cds.fna -a OceanDNA-b14012/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:09,116] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:09,117] [INFO] Task started: HMMsearch
[2023-03-16 08:51:09,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b14012/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/reference_markers.hmm OceanDNA-b14012/protein.faa > /dev/null
[2023-03-16 08:51:09,308] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:09,309] [INFO] Found 6/6 markers.
[2023-03-16 08:51:09,327] [INFO] Query marker FASTA was written to OceanDNA-b14012/markers.fasta
[2023-03-16 08:51:09,330] [INFO] Task started: Blastn
[2023-03-16 08:51:09,330] [INFO] Running command: blastn -query OceanDNA-b14012/markers.fasta -db /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/reference_markers.fasta -out OceanDNA-b14012/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:09,831] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:09,833] [INFO] Selected 6 target genomes.
[2023-03-16 08:51:09,833] [INFO] Target genome list was writen to OceanDNA-b14012/target_genomes.txt
[2023-03-16 08:51:09,838] [INFO] Task started: fastANI
[2023-03-16 08:51:09,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ceab5f4-3a87-4da3-898f-cc5a2e6753de/OceanDNA-b14012.fa --refList OceanDNA-b14012/target_genomes.txt --output OceanDNA-b14012/fastani_result.tsv --threads 1
[2023-03-16 08:51:13,350] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:13,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:13,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:13,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:13,351] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:13,351] [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 08:51:13,353] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14012/tc_result.tsv
[2023-03-16 08:51:13,353] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:13,353] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:13,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/checkm_data
[2023-03-16 08:51:13,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:13,361] [INFO] Task started: CheckM
[2023-03-16 08:51:13,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14012/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14012/checkm_input OceanDNA-b14012/checkm_result
[2023-03-16 08:51:39,234] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:39,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:39,269] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:39,269] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:39,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14012/markers.fasta)
[2023-03-16 08:51:39,270] [INFO] Task started: Blastn
[2023-03-16 08:51:39,271] [INFO] Running command: blastn -query OceanDNA-b14012/markers.fasta -db /var/lib/cwl/stg39181c1d-f53f-4366-9a26-ef8c2336d8f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14012/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:39,979] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:39,983] [INFO] Selected 18 target genomes.
[2023-03-16 08:51:39,984] [INFO] Target genome list was writen to OceanDNA-b14012/target_genomes_gtdb.txt
[2023-03-16 08:51:40,007] [INFO] Task started: fastANI
[2023-03-16 08:51:40,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ceab5f4-3a87-4da3-898f-cc5a2e6753de/OceanDNA-b14012.fa --refList OceanDNA-b14012/target_genomes_gtdb.txt --output OceanDNA-b14012/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:47,184] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:47,187] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:51:47,187] [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_003213095.1	s__AG-426-M11 sp003213095	76.2646	50	522	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__AG-426-M11	95.0	97.10	96.18	0.80	0.72	9	-
--------------------------------------------------------------------------------
[2023-03-16 08:51:47,190] [INFO] GTDB search result was written to OceanDNA-b14012/result_gtdb.tsv
[2023-03-16 08:51:47,194] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:47,196] [INFO] DFAST_QC result json was written to OceanDNA-b14012/dqc_result.json
[2023-03-16 08:51:47,197] [INFO] DFAST_QC completed!
[2023-03-16 08:51:47,197] [INFO] Total running time: 0h0m48s