[2023-06-13 09:49:02,824] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:49:02,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:49:02,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e47b3e-d741-460d-9b70-e757c62f1fc9/dqc_reference
[2023-06-13 09:49:04,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:49:04,156] [INFO] Task started: Prodigal
[2023-06-13 09:49:04,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg45f43398-6d06-4716-a714-4b63cca507ed/GCA_947458995.1_RE-16jun15-144_genomic.fna.gz | prodigal -d GCA_947458995.1_RE-16jun15-144_genomic.fna/cds.fna -a GCA_947458995.1_RE-16jun15-144_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:49:05,600] [INFO] Task succeeded: Prodigal
[2023-06-13 09:49:05,601] [INFO] Task started: HMMsearch
[2023-06-13 09:49:05,601] [INFO] Running command: hmmsearch --tblout GCA_947458995.1_RE-16jun15-144_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e47b3e-d741-460d-9b70-e757c62f1fc9/dqc_reference/reference_markers.hmm GCA_947458995.1_RE-16jun15-144_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:49:05,764] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:49:05,766] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg45f43398-6d06-4716-a714-4b63cca507ed/GCA_947458995.1_RE-16jun15-144_genomic.fna.gz]
[2023-06-13 09:49:05,783] [INFO] Query marker FASTA was written to GCA_947458995.1_RE-16jun15-144_genomic.fna/markers.fasta
[2023-06-13 09:49:05,784] [INFO] Task started: Blastn
[2023-06-13 09:49:05,784] [INFO] Running command: blastn -query GCA_947458995.1_RE-16jun15-144_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e47b3e-d741-460d-9b70-e757c62f1fc9/dqc_reference/reference_markers.fasta -out GCA_947458995.1_RE-16jun15-144_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:06,276] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:06,280] [INFO] Selected 0 target genomes.
[2023-06-13 09:49:06,281] [INFO] Target genome list was writen to GCA_947458995.1_RE-16jun15-144_genomic.fna/target_genomes.txt
[2023-06-13 09:49:06,281] [ERROR] File is empty. [GCA_947458995.1_RE-16jun15-144_genomic.fna/target_genomes.txt]
[2023-06-13 09:49:06,281] [ERROR] Task failed. No target genome found.
[2023-06-13 09:49:06,281] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:49:06,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e47b3e-d741-460d-9b70-e757c62f1fc9/dqc_reference/checkm_data
[2023-06-13 09:49:06,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:49:06,301] [INFO] Task started: CheckM
[2023-06-13 09:49:06,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947458995.1_RE-16jun15-144_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947458995.1_RE-16jun15-144_genomic.fna/checkm_input GCA_947458995.1_RE-16jun15-144_genomic.fna/checkm_result
[2023-06-13 09:49:19,320] [INFO] Task succeeded: CheckM
[2023-06-13 09:49:19,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:49:19,350] [INFO] ===== Completeness check finished =====
[2023-06-13 09:49:19,351] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:49:19,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947458995.1_RE-16jun15-144_genomic.fna/markers.fasta)
[2023-06-13 09:49:19,351] [INFO] Task started: Blastn
[2023-06-13 09:49:19,352] [INFO] Running command: blastn -query GCA_947458995.1_RE-16jun15-144_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e47b3e-d741-460d-9b70-e757c62f1fc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_947458995.1_RE-16jun15-144_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:19,807] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:19,813] [INFO] Selected 3 target genomes.
[2023-06-13 09:49:19,813] [INFO] Target genome list was writen to GCA_947458995.1_RE-16jun15-144_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:49:19,817] [INFO] Task started: fastANI
[2023-06-13 09:49:19,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f43398-6d06-4716-a714-4b63cca507ed/GCA_947458995.1_RE-16jun15-144_genomic.fna.gz --refList GCA_947458995.1_RE-16jun15-144_genomic.fna/target_genomes_gtdb.txt --output GCA_947458995.1_RE-16jun15-144_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:20,508] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:20,512] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:49:20,512] [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_002288365.1	s__Planktophila limnetica	81.5564	138	190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.17	97.12	0.96	0.96	5	-
GCA_009699825.1	s__Planktophila sp009699825	81.1977	105	190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.12	98.92	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-13 09:49:20,515] [INFO] GTDB search result was written to GCA_947458995.1_RE-16jun15-144_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:20,516] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:20,518] [INFO] DFAST_QC result json was written to GCA_947458995.1_RE-16jun15-144_genomic.fna/dqc_result.json
[2023-06-13 09:49:20,518] [INFO] DFAST_QC completed!
[2023-06-13 09:49:20,519] [INFO] Total running time: 0h0m18s