[2023-03-19 01:38:53,854] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,856] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference
[2023-03-19 01:38:54,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:54,945] [INFO] Task started: Prodigal
[2023-03-19 01:38:54,945] [INFO] Running command: cat /var/lib/cwl/stgaa5db482-de3a-49b5-9eea-27f19b71e960/OceanDNA-b2561.fa | prodigal -d OceanDNA-b2561/cds.fna -a OceanDNA-b2561/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:38:59,152] [INFO] Task succeeded: Prodigal
[2023-03-19 01:38:59,152] [INFO] Task started: HMMsearch
[2023-03-19 01:38:59,152] [INFO] Running command: hmmsearch --tblout OceanDNA-b2561/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/reference_markers.hmm OceanDNA-b2561/protein.faa > /dev/null
[2023-03-19 01:38:59,333] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:38:59,333] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgaa5db482-de3a-49b5-9eea-27f19b71e960/OceanDNA-b2561.fa]
[2023-03-19 01:38:59,344] [INFO] Query marker FASTA was written to OceanDNA-b2561/markers.fasta
[2023-03-19 01:38:59,344] [INFO] Task started: Blastn
[2023-03-19 01:38:59,344] [INFO] Running command: blastn -query OceanDNA-b2561/markers.fasta -db /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/reference_markers.fasta -out OceanDNA-b2561/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:38:59,905] [INFO] Task succeeded: Blastn
[2023-03-19 01:38:59,907] [INFO] Selected 22 target genomes.
[2023-03-19 01:38:59,907] [INFO] Target genome list was writen to OceanDNA-b2561/target_genomes.txt
[2023-03-19 01:38:59,925] [INFO] Task started: fastANI
[2023-03-19 01:38:59,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa5db482-de3a-49b5-9eea-27f19b71e960/OceanDNA-b2561.fa --refList OceanDNA-b2561/target_genomes.txt --output OceanDNA-b2561/fastani_result.tsv --threads 1
[2023-03-19 01:39:10,691] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:10,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:10,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:10,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:10,692] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:10,692] [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
--------------------------------------------------------------------------------
[2023-03-19 01:39:10,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2561/tc_result.tsv
[2023-03-19 01:39:10,693] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:10,693] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:10,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/checkm_data
[2023-03-19 01:39:10,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:10,700] [INFO] Task started: CheckM
[2023-03-19 01:39:10,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2561/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2561/checkm_input OceanDNA-b2561/checkm_result
[2023-03-19 01:39:27,530] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:27,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:27,558] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:27,559] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:27,559] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2561/markers.fasta)
[2023-03-19 01:39:27,560] [INFO] Task started: Blastn
[2023-03-19 01:39:27,560] [INFO] Running command: blastn -query OceanDNA-b2561/markers.fasta -db /var/lib/cwl/stg54771b2a-6e52-4852-ae53-19a06c9e92a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2561/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:28,428] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:28,430] [INFO] Selected 17 target genomes.
[2023-03-19 01:39:28,430] [INFO] Target genome list was writen to OceanDNA-b2561/target_genomes_gtdb.txt
[2023-03-19 01:39:28,488] [INFO] Task started: fastANI
[2023-03-19 01:39:28,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa5db482-de3a-49b5-9eea-27f19b71e960/OceanDNA-b2561.fa --refList OceanDNA-b2561/target_genomes_gtdb.txt --output OceanDNA-b2561/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:33,824] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:33,827] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:39:33,827] [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
GCF_000257665.1	s__Aquiluna sp000257665	86.3694	198	212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182225.1	s__Aquiluna sp905182225	85.1333	167	212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854485.1	s__Aquiluna sp017854485	76.9009	50	212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:39:33,828] [INFO] GTDB search result was written to OceanDNA-b2561/result_gtdb.tsv
[2023-03-19 01:39:33,830] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:33,832] [INFO] DFAST_QC result json was written to OceanDNA-b2561/dqc_result.json
[2023-03-19 01:39:33,832] [INFO] DFAST_QC completed!
[2023-03-19 01:39:33,832] [INFO] Total running time: 0h0m40s